A carpet of sand stretches into the distance below me. As clear and still as the water, the light seems muted, creating a peaceful, subdued scene.

Surrounding each rocky feature are small oases of life. At one, there are two nudibranchs (sea slugs) and, as I swim closer, I become aware of a tiny goby on a strand of coral, so camouflaged as to be practically invisible. The long, effortless dive seems to last forever and throughout, I catch glimpses of species I’ve never seen before.

When it comes to scuba diving in Asia, countries such as Malaysia or Thailand garner the most attention, but Japan is a hidden gem, with dive spots across the country. The far north is cold, with seaweed and rocky topography, while the south offers shallow coral reefs, slopes, sheer walls and carpets of white sand. Conditions vary widely and, with over 3,000 species of fish inhabiting the archipelago, there is a vast collection of marine life.

That one country can offer such underwater variety is what I love about diving in Japan. Below is a tiny collection of dive sites among the many the country has to offer.

Izu Islands, Tokyo Pref.

Although they’re under the jurisdiction of the Tokyo Metropolitan Government, the Izu Islands are worlds apart from the frenzy of Tokyo. Subtropical Hachijojima island is formed by two adjacent volcanoes. The warm Kuroshio current meanders past, bringing with it life and offering encounters with coral, sea turtles and yūzen (wrought-iron butterflyfish), a species endemic to the area.

Low life: A Japanese pygmy sea horse off the coast of Hachijojima island, an overnight ferry ride from Tokyo.
Low life: A Japanese pygmy sea horse off the coast of Hachijojima island, an overnight ferry ride from Tokyo. | KOTARO TANAKA

One of the most popular sites is Nazumado, home to a submerged ledge with an arch in the middle. Colorful reef fish congregate in clouds, while some sections shelter lionfish and yellowfin soldierfish. Crevices, cracks and wall formations have built up over centuries, full of anemones and moray eels. A huge hit among divers, Japanese pygmy sea horses are also seen frequently, while nudibranchs are just as popular.

The rugged coastline of Izu Oshima, the closest of the Izu Islands to the mainland, is just as impressive. One of the best ways to wake up after the overnight ferry from Tokyo is to jump into the water at Akinohama and enjoy its collection of boxfish, clownfish or the odd cuttlefish. But other, more dramatic encounters await — swim into the blue before sunrise at Keikai and hang off the walls. Chances are you’ll spot the weird and wonderful hammerhead shark. On my last visit, we hadn’t been waiting 10 minutes when a small shiver cruised past. They were too far away and the current was too strong for photographs, but it was an incredible encounter.

Diving in the Izu Islands: Jim Goddard of Discovery Divers Tokyo runs trips to Hachijojima and the Izu islands in the summer. Kotaro Tanaka of Concolor is a keen underwater photographer and dive guide off Hachijojima.

Oki Islands, Shimane Pref.

Located in the Sea of Japan, the Oki Islands are the remnants of an ancient volcano and collectively form a UNESCO Global Geopark. At first glance, the underwater world seems plain and, as I was guided to a gloomy looking entrance at Katado, I wasn’t particularly excited. But I was in for a surprise. Sunbeams penetrated the deep waters, and throughout the dives, my guide acted as a spotter, using his torch to point out macro subjects such as lionfish and nudibranchs.

Cave diving: Located in the sea of Japan, the Oki Islands are part of a UNESCO Global Geopark.
Cave diving: Located in the sea of Japan, the Oki Islands are part of a UNESCO Global Geopark. | EIJI YANAGIHARA

The Dozen Islands (Nishinoshima, Nakanoshima and Chiburijima) offer the most marine life variety. Enter the water off Nishinoshima and you’ll see schooling yellowtail amberjack, significant shoals of damselfish and leafy green seaweed offering sanctuary to orange starfish, jawfish and crabs.

Thirty minutes away off the northeast coast is the tiny island of Hoshi no Kami (Star Goddess Island), where moderate currents flow past exposed outcrops, bringing nutrients to a thriving marine community: colorful sponges, sea slugs and curious-looking blennies nestled in the nooks and crannies.

The Dozen Islands are a caldera with an unusual combination of geological features including vast cliffs, arches and caves sculpted over millions of years. Underwater, this is plain to see, with pinnacles, crevices and a unique topography hosting bags of marine life.

Diving in the Oki Islands: Eiji Yanagihara of Club Noah Oki offers diving and kayak tours. Contact Maia Lee at the Nishinoshima Tourism Association for information in English.

Kushimoto, Wakayama Pref.

The sea off Kushimoto is treacherous in typhoon season but the sheer weight of life in these waters make it a world of color where fish flutter in and out of the soft coral, rocks and sponge growth. Located on the southern curve of Wakayama Prefecture, Kushimoto offers some of Honshu’s most vibrant diving.

A spotted and barred blenny peers out from its home in Kushimoto.
A spotted and barred blenny peers out from its home in Kushimoto. | NAOFUMI UEDA

At the Black Tunnel, an arch stretches between two huge rocks. Crabs cling to the walls or nestle in crevices. Schools of sea goldies and butterfly fish circle in the open water. Look closely and you’ll find tiny starfish and nudibranchs. The Black Tunnel begins at around 32 meters, so the dive is short and a minimum of PADI Advanced Open Water training (or equivalent) is required.

Nagizaki, off the island of Kii Oshima near Kushimoto, charms visitors with a rock formation that is an oasis for a range of marine life. Red fans and yellow sponges decorate the area. The rock walls are nothing short of spectacular, so make sure your torch is fully charged as there are lots of holes and crevices to investigate.

Eels have breached the area, peering out from within as they wait for the ideal moment to ambush their prey. Tiny delicate anemone shrimps can also be found waiting and watching among the flowing tentacles of their homes.

Diving in Kushimoto: Naofumi Ueda at Dive Kooza offers a range of boat dives off Kushimoto and freshwater dives in nearby rivers.

Yakushima, Kagoshima Pref.

Visitors to the island of Yakushima are usually drawn to the lush, green forests and hiking trails. But underneath this temperate ecosystem is another world.

Yakushima’s north coast has some key dive sites, including Zero-sen Isso, the resting place of a long-range fighter aircraft. The structure is ablaze with sponges and bright algae, so much so that every tiny section seems colonized by something.

Creatures of the deep: Yakushima is famous for sea turtles, but also for stranger looking animals such as cuttlefish.
Creatures of the deep: Yakushima is famous for sea turtles, but also for stranger looking animals such as cuttlefish. | SHIGERU HARAZAKI

As Japan’s premier nesting site for turtles, it is also no surprise to encounter the elegant creatures off Yakushima. The north coast also has various signature species. Scorpionfish, lionfish and Moorish idols all make appearances, as well as bigger animals like sea snakes hunting among the corals.

Diving in Yakushima: Shigeru Harazaki at Yakushima Diving Service Mori to Umi is a veteran underwater photographer who offers regular guided dives.

Miyakojima, Okinawa Pref.

For winding, limestone arches, horizontal tunnels and swim-throughs, the island of Miyakojima is the place to go. Gakeshita houses a large rock surrounded by smaller ones that divers can meander through. The walls are splashed with anemones, soft coral and encrusted sponges, while species such as purple queens, peach fairy basslets and shaded batfish swirl by.

Sea slug: A brightly colored nudibranch in Miyakojima island
Sea slug: A brightly colored nudibranch in Miyakojima island | YORKO SUMMER

By far one of my favorite species in Miyakojima is the tiny candy crab that mimics the coral it sits on and attaches coral polyps to its carapace for camouflage. Poised with my camera, I’ve often tried in vain to get a decent shot, but when they are considerate, they make the most enjoyable subjects, slipping down beneath their soft coral castle as they attempt to hide away.

This year, Miyakojima is marking the third International Year of the Reef (IYOR 2018) through marine conservation activities such as beach cleans and its Eco Island Contest.

Diving in Miyakojima: Hiroyuki Kimura and his family run Dive Kids and offer regular guided dives.

Ishigaki Island, Okinawa Pref.

Just 3½ hours away from Tokyo by plane is one of Japan’s undoubted underwater jewels. The sea off Okinawa Prefecture’s Ishigaki Island is full of life and, with the help of guides, it’s easy to navigate and find a range of coral reef inhabitants.

The steep, sloping Osaki Hanagoi Reef (Anthias Reef) is named after the anthias fish synonymous with tropical reefs. Clouds of them swirl above the coral, while other species such as angelfish and butterfly fish congregate along the bottom. With few natural predators, they seem fearless and appear to nonchalantly pose for images.

A manta rays soars gracefully over Manta Scramble on Ishigaki Island.
A manta rays soars gracefully over Manta Scramble on Ishigaki Island. | OSCAR BOYD

Ishigaki is perhaps most famous for manta rays that appear between July and November. These harmless giants gently hover over the rocks at Manta Scramble, waiting for cleaner wrasses to remove unwanted parasites from their bodies. Manta Scramble is a fascinating dive, but even more exciting is the anticipation of reaching it. Huge structures arise from the seafloor, into which divers settle as calmly as possible, staying low to avoid interfering with the mantas as they glide elegantly by. It’s a diver’s dream and a transcending moment to get so close to these gentle and immense creatures.

Diving in Ishigaki: Koichiro Chiwata of Prime Scuba Ishigaki offers regular full day dive programs for beginners to experts.

Bonnie Waycott lived in Tokyo between 2006 and 2017 as a writer and researcher of Japan’s aquaculture. For more tips on diving in Japan, her blog can be found at bonniewaycott.com. Please note, while this article endeavored to list dive shops with some experience of non-Japanese divers, the majority of shops and guides in Japan do not speak English and you should plan accordingly.

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