Three Awesome Indonesian Dive Sites

If you want to see tropical marine species in their native habitat, Indonesia ranks as a top spot.

A juvenile yellow mimic tang (acanthurus pyroferus). Photo by Scott W. Michael
A juvenile yellow mimic tang (acanthurus pyroferus). Photo by Scott W. Michael

Indonesia is home to some of the most impressive reef faces in the world.

Keeping marine aquariums and exploring the underwater world with scuba or snorkeling gear are two past times that often go hand in hand. No, you don’t have to be a diver to appreciate and enjoy keeping marine aquariums, but observing marine organisms in their natural habitat will add an additional dimension to your saltwater infatuation. It was marine fishkeeping that inspired me to don a mask, snorkel and explore coral reefs. It has been my good fortune that since those early snorkeling experiences, I have been able to spend many hours underwater, observing and photographing coral reef inhabitants.


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I am often asked, “What’s your favorite place to go diving?” This is a difficult question to answer because it is dependent on the inquisitor’s specific interests. Do they want to experience clear water and beautiful reefs? Do they want to see lots of unusual critters? Or are they fans of charismatic megafauna, such as sharks, mantas and marine mammals? If the questioner is like me and is into variety, then I will always recommend the Indonesian Archipelago. In this article, we will look at what makes Indonesia so special.

A Land of Diversity

Indonesia is a diverse utopia. There are approximately 18,585 islands in the Indonesian Archipelago, and the coastlines of many of these support rich coral reefs. Along with the Philippines, Indonesian waters boast the greatest variety of invertebrate and fish species in the world. Indonesia is the epicenter of what scientists have labeled the “Coral Triangle” — a geographical region that is the “cradle” of marine biodiversity. Why are Indonesian waters such a “species factory?” The key ingredients are a long evolutionary history and a wide variety of marine habitats. This includes fringing reefs, drop-offs, platform reefs, coral cays, mangrove forests, sea grass meadows, sand flats, estuaries and areas with cold water upwellings, etc.

arminia dermatobranchus

Arminia dermatobranchus. Photo by Scott W. Michael

If you are a “coral geek,” you will find no better place to dive or snorkel than Indonesia. More than 600 species of stony corals have been reported from this region. Members of the genus Acropora, Diploastrea, Favia, Favites, Platygyra and Porites are some of the dominant stony corals on Indonesian fringing reefs, while the genera Echinophyllia, Fungia, Montipora, Pachyseris, Pavona and Pectinia are also well-represented. In the more unusual habitats, such as muddy bays or slopes, one can find more atypical large-polyped stony corals like Cynarinia, Scolymia and Trachyphyllia. Soft coral also abound on Indonesian reefs. Some of the more ubiquitous soft coral genera include tree corals (Litophyton spp.), leather corals (Sarcophyton spp.) and finger-leather coral (Sinularia spp.). You can also find the beautiful Dendronephthya and Scleronephthya corals, which typically occur under dome-shaped Porites corals, in caves and under ledges. Soft corals in the genera Xenia, Pachyclavularia and a variety of gorgonians are also seen. Large sea anemones are common on some Indonesian reefs, many of which harbor their anemonefish, as well as shrimp symbionts.

While the number of corals in this island group is impressive, the number of fish speciation in Indonesia is utterly mind-blowing! It is estimated that about 2,200 fish species (in more than 113 families) are found around Indonesian reefs, with new species being discovered all the time. The 10 most specious families are the gobies (272 species), wrasses (178), damselfish (152), cardinalfish (114), blennies (107), groupers (102), morays (61), seahorses/pipefish (61), butterflyfish (59) and snappers (43 ). Only about 5 percent of the species are endemic to the Indonesian Archipelago. Some noteworthy endemic Indonesian fish include Walea pygmy seahorse (Hippocampus waleananus), Dinar’s dottyback (Pictichromis dinar), Erdmann’s dottyback (Pseudochromis erdmanni), flaming dottyback (P. matahari), Mooi’s dottyback (P. mooii), spot-stripe dottyback (P. tonozukai), dusky fairy wrasse (Cirrhilabrus brunneus), whipfin fairy wrasse (C. filamentosus), Naokaoae fairy wrasse (C. naokoae), redhead wrasse (Halichoeres rubricephalus), Saowisata wrasse (H. binotopsis), yellowfin flasher wrasse (Paracheilinus flavianalis), blue shrimpgoby (Myersina sp.) and Bath’s blenny (Ecsenius bathi).

Top Spots

With thousands of islands and a stunning array of different habitats to explore, the number of dive sites in this region are as plentiful as the stars in the heaven! OK, maybe I am engaging in a bit of hyperbole here, but there are truly hundreds of places to dive in Indonesia. Because of space limitations, I will restrict this survey to three places in the Archipelago that I believe will be of special interest to those that keep marine aquariums.

antennarius pictus

A juvenile antennarius pictus. Photo by Scott W. Michael

Tulamben, Bali

One of the best-known islands in this archipelago, and easiest Indonesian isles to get to, is the island of Bali. It is situated nearly smack dab in the middle of the Archipelago, being bordered by Java to the west and Lombok to the east. It is well-known for its volcanoes, Hindu temples, lavish hotels and fantastic underwater scenery. Fringing and bank reefs are the two reef types found around Bali. In some areas of the coastline, there are cool, deep-water, upwellings and strong currents that influence shallow-water communities. Drop-offs with rich coral growth are found in some areas, while steep sand slopes adorned with patch reefs are common. There are several shipwrecks, seagrass beds, mangrove swamps and estuaries that provide sanctuary for invertebrates and fish as well. Some of these locations (e.g., Secret Bay) are renowned “critter” or “muck” diving sites. Much of the substrate around Bali reefs is composed of volcanic or black sand. Sedentary fish that live on this darker substrate, like shrimpgobies, often display more intense coloration than on a lighter background.

Checkered dottyback

Checkered dottyback (Cypho zaps). Photo by Scott W. Michael

One of my favorite dive sites in Bali is an area known as Tulamben, which is located on the east coast of the island. It is a site that features a 390-foot ship wreck, the Liberty — a United States army cargo ship that was torpedoed by the Japanese in WW II. The wreck is encrusted with beautiful soft corals and is home to thousands of fish. (Beware of the stinging hydroids on the superstructure!) One downside of Tulamben is that it is readily accessible to aquanauts, and as a result, it is often overrun by snorkelers and divers during late morning to mid-day. I suggest staying at one of the affordable hotels in the area and diving the wreck early in the morning and later in the afternoon. When the wreck is crawling with divers, explore the black sand slopes and limestone outcroppings.

The marine life on the wreck and surrounding habitats can be mind-blowing. On the sand slopes, there are scattered patch reefs that harbor reef-associated species, while the black sand is home to both the familiar (e.g., shrimpgobies, jawfish) and less commonly encountered sand-dwellers (e.g., snake eels, stargazers). Look for the flasher wrasses (Paracheilinus spp.) around rubble and sponge patches. If you descend down the slope, you may even encounter the ocean sunfish (Mola mola), which visits this area in order to be “serviced” by cleaner fish like the schooling bannerfish (Heniochus diphreutes). There is also a wall on the east side of the bay that is home to luxuriant Montipora growth and a typical Indonesian reef fish assemblage (e.g., butterflyfish, angels, surgeonfish, puffers, triggers). Inshore from the wall, you will find a rocky bottom where you might encounter a foraging reef octopus (Octopus cyanea). As these cephalopods feed, they are often escorted by an entourage of opportunistic piscine predators like groupers, goatfish and wrasses. This is a great place to snorkel.

Amphirprion melanopus

A clownfish (Amphirprion melanopus) in the host anemone. Photo by Scott W. Michael

Bali diving tends to be more affordable than many other dive sites in Indonesia. There are more varied accommodations (including budget hotels/hostels), and it is easier to get to Bali from many places on the planet, which means it takes less time to get to Bali, and the cost of air travel tends to be less expensive. The best time to go to Bali is April to July and October and November (January and February are the monsoon seasons). You can participate in day dives at various sites along the coast or do a multiple-day, liveaboard trip. The dive sites vary in the level of dive experience required, and it will be important that you do your research and find a good dive operator in the area.

Lembeh Strait, Sulawesi

Sulawesi, formerly known as the Celebes, is one of the largest islands in the Indonesian Archipelago, covering an area of about 73,000 square miles. Its extensive coastline is fringed, in many areas, by coastal reefs teeming with marine life. Lembeh Strait is located on the northeastern coast of Sulawesi and separates the main island and the much smaller isle of Lembeh.

In the dive community, Lembeh Strait has become known as the “Macro-Mecca.” This is because of the incredible number of unusual marine animals that are regularly encountered in this area. Animals like mimic octopuses, flamboyant cuttlefish, sea slugs, Bobbit worms, snake eels, ghost pipefish, seahorses (including pygmy species), waspfish, a mix of lionfish, other scorpionfish, devilfish, stonefish, crocodilefish, mandarin dragonets and shrimpgobies are seen here with greater frequency than most other dive destinations. If you like frogfish, Lembeh is the best spot to find them on the planet! I have seen nine different species here, and at a number of the sites, you are likely to see four or five individuals on a single dive. It is also a great place to find symbiotic animal pairings. For example, you will see a number of crustaceans that live on corals, jellies, seastars and sea urchins. Another species that is somewhat unique to this area (and the island for which they are named) is the Banggai cardinalfish (Pterapogon kauderni). Having been referred to as “reef rats” because of their invasive nature, a small population of P. kauderni was introduced to the water’s of Lembeh. Now they are abundant in most shallow-water habitats, where the sea anemones and/or urchins in which these cardinalfish prefer to live are also found.

Crocea clam

Crocea clam (Tridacna crocea). Photo by Scott W. Michael

Many of the dives are conducted on sand slopes (Retak Larry, Denise’ Hair Ball, Jahir, to name a few) that are devoid of much reef topography. Instead, you investigate clumps of algae and sponge or small patches of reef and rubble. But there are some well-developed reefs here, as well as some unique coral communities. For example, there are large stands of hammer coral (Euphyllia ancora) that cover hundreds of square yards (Kungkungan Bay Resort House Reef). There are “fields” of elegance corals (Catalaphyllia elegans) on black sand slopes (Jahir) and there are beautiful Montipora gardens in a shallow protected inlet (Lettuce Surprise You).There are also a couple of interesting wrecks and pier piling dives. One thing you must do when visiting Lembeh is night dive. All of kinds of bizarre creatures erupt from the sand after dark, making it one of the best places for nocturnal exploration that I have ever seen.

When I first starting visiting this area, there was only one resort on Lembeh Strait; now, there are at least six. There are also live-aboard boats that regularly spend time in Lembeh Strait. Getting to Lembeh is fairly easy. Flights regularly go from Singapore to Manado; from there, you are transported by vehicle to your resort (this road trip is likely to be the scariest part of your Lembeh vacation). You can dive Lembeh all year round, with September to October typically being considered the best period. Be prepared for cold water in July and August.

Raja Ampat Islands, West Papua

West Papua, formerly known as Irian Jaya, is a province of Indonesia. It consists of the western peninsula of the island of New Guinea and extends to the Birds Head peninsula and the Raja Ampat Islands in the west. The Raja Ampats are fantastic above and below the water. The area consists of several large rainforest-laden islands and approximately 1,500 cays and smaller islets. Many of these limestone islets have eroded into exquisite shapes (this geological phenomenon is known as drowned karst topography). Some look like giant beehives, whiles others resemble massive mushrooms. The archipelago and the surrounding ocean environs covers an area of more than 150,000 square miles and include open-ocean, platform reefs to highly sheltered, fringing reefs in sheltered lagoons and around numerous islets. There are also many mangrove areas, including some that are flooded by clear seawater, making for unique photographic opportunities.

When it comes to fish diversity, West Papua is the most stunning jewel in Indonesia’s crown. The Bird’s Head Peninsula, which includes the Raja Ampat Islands, boasts one of the richest reef fish faunas on the planet, with more than 1,500 species representing 111 families reported so far. For such a small region, it also has a large number of endemic fish – 26 species in 14 families. This includes three species of epaulette sharks (Hemiscyllium spp.), two of which were recently discovered, four species of dottybacks (Pseudochromidae) and three wrasses (two Paracheilinus and one Cirrhilabrus). For shrimpgoby lovers, there are 32 species that have been reported from this region! The Raja Ampats are also home to at least four pygmy seahorse species (including the rare red and white form of Denise’s pygmy seahorse [Hippocampus denise]).

For you coral lovers, surveys have counted more stony coral species around the Raja Ampats than any other region in the world. They recorded 456 species (including more than 60 Acropora spp. and 30 Montipora spp. alone) and concluded that around 96 percent of the scleractinians reported in Indonesia occur in the Raja Ampats. The mollusk biologists also reported amazing numbers. They identified 699 species, including 530 gastropods, 159 bivalves and five cephalopods. This was more than previous surveys recorded in Indonesian locations, the Philippines and Papua New Guinea. How about crustaceans? A staggering 57 species of reef-associated mantis shrimps are known from the Raja Ampats. Once again, this incredible biodiversity is a function of the amazing array of habitats available.

The Raja Ampats are not only home to small sea creatures, one of the most famous sites (Manta Sandy) features one of the biggest fish in the sea. This site is located near a small coral cay, which has fringing reef surrounding it. The area is popular for the awe-inspiring manta rays that are drawn there by the services provided by cleaner wrasses and Klein’s butterflyfish (Chaetodon kleinii). These cleaners work over the cruising mantas, which slow down to the point of stalling as the little fish inspect and pick-off crustacean parasites. As far as other rays and sharks, the reefs in this region are home to the largest population of tasseled wobbegongs (Eucrossorhinus dasypogon) I have ever seen. There is also Freycinet’s epaulette shark (Hemiscyllium freycineti), which is regularly encountered on night dives. Unfortunately, pelagic sharks are rarely seen due to exploitation by international shark fisheries (this is true for much of Indonesian waters).

While I have only stayed at island-based resorts in the region, there are live-aboard dive boats that ply the glorious blue seas and will also expose you to truly amazing terrestrial scenery. You can dive here all year-round, but it is windier between June and August (live-aboards pull out of the Raja Ampats at this time). The very best time is between mid-October and mid-December. I would say that the diving in the Raja Ampats is not for the inexperienced. Much of the best dive sites are on reefs with incredible currents. That said, it is the flow of these nutrient rich waters that account for the vast species diversity. There are dive and snorkel sites that are better for the “newbie” — just make sure you let the dive instructor know what your experience level is so that they can steer you clear of the dives that are more challenging.

So, why wouldn’t you want to go explore the species-rich waters of the Raja Ampats? One of the biggest obstacles, at least for U.S. travelers, is getting there. It is usually a two- to three-day trip. Many travel to Singapore, then to Manado and then to Sorong. If you are staying at one of the resorts in the Raja Ampats, you will be transported by speed boat from Sorong to the island-based resort. Exploring the Raja Ampats is also a bit more expensive then Bali or Lembeh Strait. But the beauty, remoteness and incredible diving make the Raja Ampats worth the extra time and expense!

A Beauty Unmatched

If you are interested in observing marine life in situ, you should make plans to go to Indonesia. You will be blown away by the friendliness of the locals, the terrestrial beauty and, most importantly, the amazing variety of marine life! But be warned, diving in the “Coral Triangle” is even more addictive than keeping marine aquariums!


Scott W. Michael is an underwater photographer, author (he has written 13 books about marine animals) and veteran fishkeeper. He manages the aquarium service company, Reef Tectonics.

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