The best liveaboard diving routes in Indonesia

Indonesia Liveaboards
In Indonesia you can find some of the best liveaboards in the world, many build in traditional Indonesian style

The challenge to summarize the best liveaboards diving routes in Indonesia in only 5 in a country like Indonesia, with more than 13,000 islands, located in the heart of the Coral Triangle and having some of the best dive sites in the world, is highly complicated and, yes, we admit it, quite risky… but we will try.

These are 5 of the best diving routes in Indonesia, routes that all of them have something that makes them really unique. They are all little crowded areas and the quality and amount of sea life is extraordinary. We have only selected premium liveaboards… which does not mean that they are extremely expensive. From only USD 2,300 you can have one trip with 20 dives in one of the best places in the world like Komodo. 

In each route we have included a video. Like us, you know it’s the best way to show the highlights of every site, especially when we are talking about areas of enormous diversity, full of life and pristine reefs. Are you ready? 


This route, one of the most popular, is not where you will find the largest pelagics and in the greatest amount, but you will find a truly impressive biodiversity. If you have never dived in Indonesia this route could be a good starting point since it is considered a summary or the diving in Indonesia and the different types of fauna you can find in this country. Without forgetting a truly extraordinary dive, perhaps the most famous and valued, «Manta Alley», where you’ll dive with dozens of curious manta rays that hover within inches of your regulator wondering what are those bubbles that come out of those strange beings. We counted 18 the last time we were at that point, in the summer of 2016. This route also gives you the chance to join a shore excursion that attracts divers: the Komodo dragons. You’ll be able to see them up close (and even smell them) in the National Park of Komodo.

This route is subject to changes and variations, like all the routes that you’ll see in this article. But basically departures from Bali visiting the Komodo Park and returning to Bali it could arrive to Labuan Bajo spending a couple or three more days on the south of Komodo. There are several interesting combinations to dive in Komodo, both north and south of the Park and it is worth studying before booking your liveaboard holidays.

The Komodo National Park, the heart of this route, is home to more than 1,000 species of fish, 260 species of corals and 70 species of sponges. On this route you will find easy and relaxed diving in shallow reefs, in warm water, calm and full of color coral gardens… but also drifting dives besides walls full of corals where you don’t see the bottom, visits of black tips sharks, grey sharks, white tip sharks, or giant sunfish. You will also dive with extreme currents where you just have to let yourself go with it like in the dive site «Shotgun». Here in Komodo you will also have the opportunity to see dolphins and some whales if you are lucky enough.

In Komodo you should not miss a single night dive, ideal time to discover the amount of food that goes through these islands, plagued with plankton, and where you can see lots of frogfish, orangutan crabs, flamboyant cuttlefish, loads of Spanish dancers (with impressive sizes), pygmy seahorses… to en the dive and find yourself under a sky full of stars in one of the most remote areas and farthest from the light where one can dive. What else can you ask for? 

komodo diving
Komodo National Park is full of huge coral gardens where from time to time you’ll find nice surprises. Pic by Alex Lindbloom from Mermaid II Liveaboard

The cruise usually starts on Moyo Island for a check dive in «Angel Reef» where it is very possible that a curious a black tip shark that lives there will come to check you out. Among the large number of sponges there are turtles, a large number of surgeons, eels or an occasional sea serpent searching for food among the holes in the reef, huge moray eels…

Before getting into the Komodo National Park some really interesting dives take place but it is in the National Park where the coral gardens begin to become bigger and bigger, the huge schools of fish get bigger, more and more turtles you’ll see, the sea fans are wider, some black corals start to appear in the depth…

This route is suitable for all levels, and will be enjoyed by both macro and wide-angle lovers. It is ideal for those divers who continue to be moved by feeling like children searching through rocks and corals finding amazing invertebrates and small, colorful fish… and I assure you that your interaction with the manta rays will be unforgettable.

Best time to dive IN KOMODO

This diving route is active throughout the year, with more cruises from May to October-November. Then many cruises go to Raja Ampat. From November to January the visibility is better, but it is during summer when there are more concentrations of food and plankton in the water and the activity, especially of manta rays, is greater. The sea is somewhat more agitated but it will not be a bigger problem than a little bit more uncomfortable cruise. 


This cruise is (usually) a 11 nights dive trip due to its long crossings. I has a mix of macro and big animals hard to match, combining the best of the Banda Sea and Misool, in the south of Raja Ampat. 

This route allows modifications according to the sea conditions and, depending on whether the cruise includes more or less nights, you can dive also in the Forgotten Islands. Departing from Ambon or Maumere the cruise will take you through the Banda Sea and the «Ring of Fire» (named for the presence of numerous active volcanoes) on a route steeped in history and blessed with some of the best dives site in Indonesia, with a vast diversity of species, both large and small. Traveling around 550 nautical miles, you will visit many different islands and a wide variety of diving sites in an area of ​​very clear and nutrient-rich waters that attract pelagic species such as giant sunfish, manta rays, hammerhead sharks, dolphins, sailfish… and if you are very luck you’ll see sperm whales or whale sharks crossing the channels.

With an amazing visibility of up to 30 meters and walls full of coral that fall hundreds of meters into the abyss, the cruise starts in Ambon, where there is excellent macro diving and a top world muck diving, with lots of scorpion fish, frog fish, cockatoo fish, many different types of leaf fish, pipe fish of different species, mimic octopus, mandarin fish, sea horses… The list is spectacular, incredible.

In Misool, one of the 4 main islands of Raja Ampat, you’ll dive in more than 9 spots where we can find from cleaning stations of manta rays to huge jacks in big schools, white tip sharks, gray sharks, wobbegong sharks, the beautiful humphead wrasse… all of them living in an environment of spectacular white and hard corals. 

A very interesting area, perhaps the most valued by lovers of strong emotions, is located in the Dampier Strait, a channel where strong currents creates a marine life blooms and where big fish feel especially comfortable: mantas, sharks, tuna, jacks and barracudas come to these areas where to hang with the reef hook to watch the ocean go by.

Pulau Manuk diving banda sea
Pulau Manuk, one of the islands of the Banda Sea, common stop in liveaboards. Image courtesy of MV Ambai

Banda Neira, the main island of Banda Islands, is an important part of this cruise. This island, one of its 10 small volcanic islands, has incredible hard coral gardens. Around the island you’ll find a few channels that flow towards the Banda Sea, completely loaded with nutrients, which guarantees a beautiful spectacle with huge schools of fish very much wished by any diver: giant groupers, big shoals of barracudas, snappers, surgeon fish or sweet lips living around beautiful corals. The currents, sometimes pretty strong, can not guarantee the best visibility, but there is a great possibility to see manta rays, hammerhead sharks, mobulas or schools of eagle rays.

Best time to dive IN BANDA SEA

The best moment to visit the Banda Islands are the months of March and April and from September to December. Outside of this time the weather is unstable and there are few liveaboards operating that route.


This route to the «Forgotten Islands is a journey through time. They are called «forgotten» because of the little contact they have had with the rest of Indonesia for centuries. Less than 1% of Indonesians inhabit the 1,000 sparsely populated islands that belong to ​​the Moluccas and extend east from Alor and reach as far as Ceram and Ambon.

Due to the changing climate and the possibility of storms in the area the itineraries of this route, up to 13 nights, can change. The cruise usually departure from Ambon, the capital of the Moluccas, and finishes in Saumlaki on Tanimbar Island but they can also start from Labuan Bajo or Saumlaki.

This cruise has the character of adventure that gives visiting areas that have only recently opened to diving cruises, diving and crossings around volcanic islands. In addition this route can be done in some of the best sailboats made with Indonesian woods in the traditional way, making this diving trip something exceptional. 

Through this route in the «Forgotten Islands» you’ll dive in some of the most extensive and intact coral reef systems that Indonesia has in its more than 850,000 sq km, with steep walls but also on comfortable slopes sheltered from the current, easy and relaxed dives but at the same time exciting and super interesting. 

As you can imagine from such a remote area, the quantity and quality of life, as you have seen in the video above, is extraordinary, both small and pelagic life: large schools of reef fish as well as frequent sightings of large tuna, barracudas, giant jacks, dog tooth tuna (Gymnosarda unicolor) that can exceed two meters, thresher sharks, white and black tip sharks, grey sharks, humphead wrasse, huge clouds of fusiliers…

Forgotten islands diving
In the Forgotten Islands we can find a high quality muck diving. Picture of Tiare Liveaboard

Among the most outstanding areas and dive sites we have to note «Nusa Laut», a reef full of beautiful corals and a great macro diving where scorpion fish, pipe fish, frog fish of a thousand types, rhinopias, blue ring octopus and larger animals like barracudas, white tip sharks, humphead wrasse, manta rays and even hammerhead sharks sometimes. Another diving area in which liveaboard stops for a couple or three dives to meet with pelagic fauna and big fish is «Koon» where a channel receiving currents will let you dive with with giant groupers, white tip sharks, manta rays, mobulas, schools of barracudas, sweet lip fish, tuna or sea snakes.

Best time to dive in THE FORGOTTEN ISLANDS

The best time to join this cruise are the months of October to late December and the months of March and April, times of less tropical rain and calmer seas, although cruises are also extended to the months of September and May, but the conditions are usually worse.


Once again we have selected a remote route, far away from overcrowding and even any kind of modern civilization. This fact usually ensures reefs in a state of incredible shape, almost immaculate, where only a few lucky divers and local fishermen come into play. During your dives along this exciting and relatively new diving route you can expect to see an incredible underwater biodiversity. Waters that arise from great depths along with currents between islands bring nutrients to the reef. And if there is life on the reef big fsh will come looking to feed on it: sunfish, thresher sharks, hammerhead sharks, dolphins, spearfishes, sailfish and even humpback and blue whales!

If you participate in this cruise it is very likely that you will embark in Maumere, on the large island of Flores in the east of Indonesia, on your way to Alor to dive in the surroundings of the islands of Kumba, Ternate and Pura (which are all in the Strait of Pantar) in the following days. The cruise continues to the islands of Marisa, Kawula, Solar and Adonara before returning to Maumere. 

On the island of Kumba there is a spectacular volcano where you can enjoy one most beautiful sunsets I’ve ever seen in Indonesia. The surrounding waters of this island allow to accumulate currents rich in nutrients that create fantastic conditions for encounters with some of the largest fish in the ocean, from white tip and grey reef sharks, to giant groupers and even whale sharks.

A curious experience will be the encounter with young fishermen (under 15 years old the most of them) with their homemade swimming goggles that dive without shoes or fins to check their fish traps. They will be happy posing for you:-) You will also find giant barrel sponges, hard corals, huge schools of crystal fish, sweet lip fish, emperor angel fish, turtles, marine snakes, innumerable cleaning stations full of blennies… 

Most of the diving cruises that make the route Flores and/or Alor make almost compulsory stops in the islands of Pulau Buaya, Ternate and Pura, three small consecutive islands located between larger islands that form a channel full of life. The water is usually colder than the rest of the route, between 20 and 22 C degrees, and you will find unforgettable dives like «The Bullet» or «Sharks Galore», loaded with sharks, turtles or mantas and where, be careful, the current can take you regulator away! A truly exciting dive where the most attractive octopus of the ocean also appear: mimic, wonderpus or blue rings are easy to find in these islands.

diving alor
The white tip sharks are very common in Alor dives. Image courtesy of Damai I

Muck diving is also first class in Alor, in areas such as the great island of Kawula, home to frog fish, all kinds of sea horses, pipe fish, commensal shrimps, boxing crabs, all kinds of nudibranchs…

Some routes include a visit to Lamalera, an area where whales and manta rays are still hunted in a traditional way, with harpoons housed in large bamboo poles. It is a meat that is eaten later in the village, of about 2,000 inhabitants. It is an unpleasant experience that many liveaboards avoid but others include it in their routes. And there is a chance, if the villagers allow it, to visit that village. Very interesting experience.

The cruise is usually comes to an end in a great muck diving area «Muck Central» in Maumere where you will be amazed with the large amount of frog fish, the incredible Ambon scorpionfish, leaffish, mandarin fish, black corals, seahorses, harlequin shrimp… an essential dive to confirm that Indonesia is one of the best (if not the best) muck diving destinations in the world.

Best time to dive IN FLORES AND ALOR

You can dive in Alor throughout the year, but the best conditions can be found from March to December. Outside of these months the surface conditions can be unstable, navigation somewhat unpleasant, and there is a greater chance of rain reducing visibility.


In Raja Ampat there are dozens of different diving routes and we could not leave it out of this selection… or choose just a single route. It had to be included because for many who know Indonesian diving very well, including the crew and guides I met in Komodo on my last trip to Indonesia, there is something in common: Raja Ampat has the best diving in Indonesia.

Why is Raja Ampat so extraordinary? Mainly because its biodiversity is even higher than other areas of Indonesia. It seems difficult to overcome areas like Komodo or Alor, but that’s the way it is. More than 1,200 species of fish, 600 of coral, almost 700 species of mollusks…

There are a lot of routes that go through and focus on Raja Ampat, with many variations from those that start and end in Sorong, those which include Lembeh and end up in Manado, some that include the Ring of Fire… Raja Ampat is a box of surprises that never ceases to amaze even those who have dived all over the world. A place where in the same dive you can see from the smallest seahorses to the largest oceanic manta rays and between them a huge variety of species of all sizes.

Generally the dives in Raja Ampat will be drifting, following the currents that fill with life the more than 1,000 small islands of Raja Ampat. Some areas have huge schools of fish and regular sightings of sharks, such as the Wobbegongs. In Mansuar it is very likely that you will find large groups of manta rays and turtles. From the boat, and often near the coast, it is possible to see families of resident dolphins and even whales!

mata ray raja ampat
Manta rays are one of the thousand attractions of Raja Ampat. Image by Indo Siren

Raja Ampat is possibly the place in the world with the greatest variety of dive sites. For example, in Misool, one of the first stops of some of the Raja Ampat diving cruises, there are more than 100 different dives and where liveaboards usually spend a couple of days, with 6 to 8 dives in total. It is an area full of pinnacles with an extraordinary density of fish, surrounded by giant gorgonians, the most colorful soft corals, pygmy sea horses, oceanic manta rays in large groups, sharks, turtles, huphead wrasse, jacks .. Also in Misool you’ll have the chance to dive in beautiful mangroves with much of the small life that will soon occupy the coral gardens and the ocean… and where occasionally a saltwater crocodile appears.

Other extraordinary dives in the cruise to Raja Ampat take place in the Dampier Strait, where a stop is made at the manta ray cleaning station where, like happens in Komodo, dozens of mantas will approach curious to play with our bubbles. In Raja Ampat you will also dive in areas of black volcanic sand where the muck diving and the macro are of a very good level: frog fish, pygmy and pontohi seahorses, blue ring octopus, nudibranchs, rhinopias…

Another curious dive takes place in Alyui Bay and its pearl farm where you can also see how they are grown. This bay also has dives with walls covered with soft corals and gorgonians with many nudibrachs and pygmy seahorses. The night dives are especially interesting where with luck you will find the curious epaulette shark (Hemiscyllium ocellatum), that small shark that seems to walk with its fins, along with wobbegongs, crocodile fish and frog fishes of different kinds and sizes.

Best time to dive IN RAJA AMPAT

Most liveaboards make the Raja Ampat route during the months of October until the end of April, although it is possible to find some liveaboards that make trips throughout the year. During the months of July and until mid-September there are strong winds and waves, which makes the boats schedule other areas to visit. The usual thing is to finish the good season of Komodo in September and start to make routes around Raja Ampat.

Any of these routes around Indonesia can become the best diving trip of your life, a trip in which you will have at your fingertips all the underwater jewels that have made you fall in love with this sport. You will dive with the largest predators and the most delicate creatures of the ocean in a wild environment, completely isolated and full of peace aboard ships where you will find dozens of strangers of which ten days later you will say goodbye as new friends with whom you share your great passions: scuba diving and the underwater world.

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