Best Diving in Japan: Into the Deep with Tips from a Local Diver

Descending into the warm waters off Okinawa’s Ishigaki Island, I might almost have been diving off Thailand or the Philippines. Below was a pinnacle covered with a light dusting of sponge and coral growth. Here, I was told to stay still, tuck in a little and wait for the show to begin.

Soon, trains of manta rays followed each other in head-to-tail formations, powering through the water with their cephalic fins spread wide and their cavernous mouths gobbling up multitudes of plankton as they glided forward with every beat of their fins. I saw them make tight circles and inhale plankton suspended in the water column, and as I watched them, awe-struck, I found it incredible that such a scene could be observed in a country like Japan.

For Japan and scuba diving just don’t seem to go together, and many divers in Asia travel to more popular, well-known destinations like Thailand or Indonesia. But Japan is blessed with some stunning underwater features and a range of dive sites that are waiting to be explored. The seas around Japan are home to stunning coral formations, fish endemic to the area and rocky seascapes illuminated by bright sunlight piercing through the water. With four main islands, over 4,000 smaller ones and a combined coastline of almost 19,000 miles, Japan’s rich and varied ocean has plenty to offer.

Amami starfish. Photo: Bonnie Waycott

Okinawa, Japan’s Tropical Paradise

Okinawa may be the crown jewel of Japan’s dive sites. The options here are endless, with rich coral reefs, white sand, hammerheads, and even some mysterious underwater ruins. In addition to Ishigaki, nearby Miyakojima Island is surrounded by smaller islets with huge limestone tunnels, rock formations and arches that open out into smaller coral beds and sandy patches. Known for its varied underwater structures, it promises divers an adventurous time.

diving in Japan - Okinawa Kerama Islands

Okinawa Kerama Islands. Photo: Bonnie Waycott

The Kerama Islands, about an hour from the Okinawa mainland, consist of three main islands (Aka-jima, Tokashiki and Zamami) and smaller, uninhabited islets, where over a thousand kinds of fish live in the crystal clear water. Marine life includes yellow boxfish, three stripe damselfish and various crustaceans. The islands have sloping reefs and shallow depths, making them suitable for beginners, while an underwater labyrinth of boulders, arches and crevasses also awaits, where turtles graze during the summer and humpbacks pass by in winter. Thanks to its high water temperatures even during the colder months, Okinawa attracts divers year-round.

Okinawa Manta Ray. Photo: Dive Shop Umicoza

Amazing Amami

The Amami Islands are an extension of Kagoshima prefecture in Kyushu, one of Japan’s main islands. The seas are home to nudibranchs of all shapes sand sizes, coral that creates a spectacular backdrop for some stunning shots, and a smorgasbord of rich, vibrant colours from reef fish fluttering here and there. Divers can also meet the jawfish, comical and entertaining with a large head, mouth and eyes, peering out from its burrow with curiosity and spitting out sand if so inclined.

Amami jawfish. Photo: Bonnie Waycott

One of the islands, Tokunoshima, is the home of a green sea turtle called Yamachan that’s been around for over 10 years. Known for his unusual mountain-like shell, he’s normally found grazing off rocks in the shallower depths.

Tokunoshima turtle Yamachan diving in Japan

Tokunoshima turtle Yamachan. Photo: Diving Service Kamui

Also worth watching in Amami is the endearing Gilbert’s cardinal fish that appears in large aggregations among the coral in sheltered lagoons and bays. Steady and focused, they’re part of a riot of activity along the many small to medium-sized rocks dotted over a carpet of white sand.

diving in Japan Amami Gilbert's cardinal fish

Amami Gilbert’s cardinal fish. Photo: Bonnie Waycott

The Lure of Tokyo

Fortunately, some of Japan’s best diving is within easy reach of the capital. As spring and summer approach, divers flock to the hot spring town of Atami. It’s not the first destination that comes to mind when looking for somewhere to dive, but a shipwreck called the Chinsen (Japanese word for shipwreck), is one of the most popular dive sites, a 120-metre cargo vessel broken in two pieces that lies at around 30m.

Its walls are covered in wide sea fans draping from opportune edges, thick coral and sponge growth, swarms of halflined cardinals and a collection of spider crabs. Stonefish and moray eels rest in the corners, while schools of orange anthias and patches of anemones live along the sides. Also near Tokyo is Miyagawa Bay on the Miura Peninsula in southeast Kanagawa Prefecture.

Miyagawa Bay nudibranch Photo: Bonnie Waycott

The bay’s waters are sometimes buffeted by mild currents, which disperse rich nutrients and attract a range of fish. Resident eels lie low, accompanied by cleaner shrimp companions, while small crabs, seahorses and a tiny harlequin shrimp also call the bay home. The biodiversity of the bay is fascinating to see, with live corals and sponges that cover the sloping rocky walls.

Atami soft coral Photo: Bonnie Waycott

Tohoku: En Route to Recovery

This region offers an entirely different underwater environment and type of diving. Among the best features are resident groups of sea urchins, abalone, scallops and patches of kelp and seaweed. The waters are also a prime breeding ground for krill shrimp, hermit crabs, small, non-commercial fish like sculpins and bitterlings, and even squid.

The sea here had long supported local people’s lives through industries such as fishing and aquaculture, but the March 11th, 2011 earthquake and tsunami changed everything. Six years on, and work to remove debris from the water continues thanks to volunteer divers who have been in the ocean almost every day since the disaster. Physical structures are being created from debris to provide food and shelter for marine communities such as abalone and scallop. The seabed is surveyed regularly, while fishermen’s boats are cleaned and repaired. A visit to Tohoku is a way of contributing to a region that’s continuing to rebuild, and offers a great understanding of just how important diving can be.

Tohoku scallops. Photo: Sanriku Volunteer Divers

Hokkaido: The Frozen Sea

A harsh environment with blizzards, icy cold winds and changeable conditions is no place for the faint of heart, and even less so for diving. Or so you would think. This is Hokkaido, Japan’s northernmost island, in the midst of winter, but its pristine ocean and mountainous landscape are still enough to draw adventurous divers. In February, frozen ice from the Sea of Okhotsk sets out on a journey.

Guided by northerly winds, it breaks up and travels south to Hokkaido’s Shiretoko Peninsula, marking the start of Japan’s ice diving season. The seabed is strewn with rocks and boulders, visibility is superb and on offer is an array of creatures — sea urchins, starfish, anemones, nudibranchs and shrimp, while the blocks of ice on the water surface above lend a dramatic quality to the whole experience. The highlight, however, is the clione or sea angel, a tiny translucent creature that hovers under the ice, flapping its wings and cute ears. If the spirit of adventure and unusual challenging diving appeals, ice diving is a must.

Japan may be more famous for Mt Fuji, temples, kimono and sushi, but its oceans are still relatively unknown. Spare a thought for the Land of the Rising Sun – with manta rays, stunning coral reefs and even diving in ice, there is much on offer in what is perhaps one of the diving world’s best-kept secrets.