Japan might not be the first place that comes to mind when you think of breath-taking marine life. But if you don’t get under water in the Land of the Rising Sun, you are missing out big time. Japan boasts some of the highest marine biodiversity in the world, and you can find anything from tiny macro life, including nudibranchs and seahorses, to the big things like sharks and manta rays.

Here is a list of the top five Japan diving spots that you’ll want to check out with their main attractions.

1. Yonaguni hammerhead sharks

yonaguni monument
Photo by Vincent Lou used under CC

Mystical, sunken ruins like Atlantis? Check. Warm, tropical waters? Check. Large schools of hammerhead sharks? Check! If diving in Yonaguni Island doesn’t amaze you, nothing will. The dive site encompasses the mysterious Yonaguni monument, a submerged pyramid-like rock formation, still debated to be either man-made monoliths or completely natural but used ritually by humans in the past.

japan diving
Photo by Oleg Dyachkin

From November to June, large schools of hammerhead sharks can be observed here on a daily basis. The resulting combination is absolutely breathtaking. You can fly to Yonaguni island, located at the southern tip of the Okinawan Islands from Tokyo, with a stopover in Naha. Sou-Wes Diving organizes dives in English and Dive Zone Tokyo also plans annual group trips.

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2. Ishigaki manta rays

I got news for you. There are no manta rays in Japan. No, they weren’t eradicated, thank god. However, what are usually advertised as manta rays to you are actually mobula rays. In this case the mobula japanica, a species of devil ray. With an average 2–3 m wingspan, they are only a bit smaller than the reef manta ray (mobula alfredi). The “manta scramble” dive point off Ishigaki Island in Okinawa almost guarantees sightings in high season from June to November. There are also off-season sightings around Ishigaki, Iriomote and Kuroshima Island.

Besides the rays, the tropical warm waters of the Yaeyama Island group harbor coral reefs and their usual inhabitants with highlights including four species of sea turtles, moray eels, sea snakes and whitetip and nurse sharks. There are tiger sharks in the area but you’d be very lucky to see one! It never happened to me, even after conducting shark survey research in the area for weeks. Low-cost airlines fly directly from Tokyo to Ishigaki daily. The island has many dive operators that offer English services, so take your pick based on positive online reviews and who speaks to you the most.

3. Mikurajima dolphins

japan diving
Photo by Oleg Dyachkin

You can dive if you want—or leave your dive gear at home; this one is also for snorkelers and free divers. And technically still in Tokyo! The Izu Islands are an overnight ferry ride from Tokyo, but still count as part of the metropolis.

One of them, Mikurajima Island, is home to a local dolphin population. These animals are completely wild but call the bays of the small island their home. Here you can find them resting during the day (dolphins never fully sleep, they always only shut one half of their brain off and stay awake and alert) and foraging at dusk and dawn. They might stay to play or simply swim past you, depending on their mood. I had some very cool interactions with these marine mammals here, swimming belly to belly with one and watching another pick up a seashell from the ocean floor and toss it to me in play. Other sightings included small stingrays, turtles and a baby hammerhead.

Several local operators can take you out on small boats to look for the pods and you can jump in with the porpoises. You can rent all gear or bring your own.

Reserve your package, including an overnight stay at a ryokan (a type of traditional Japanese inn) beforehand as it gets quite busy during the wetsuit season from June to September. We went with Keiji Kato at Umiton for a free diving trip and really enjoyed our time there. The ferry for Mikurajima Island leaves every night from Takeshiba pier in central Tokyo and arrives the next morning at the island. Dive Zone Tokyo also plans annual group trips for the dive with dolphins experience.

4. The Tateyama shark scramble

Photo by Kan Shiota, Bommie Dive

What if I told you that there was a shark-feeding dive, just a 2.5 hour train ride from Tokyo? Banded houndsharks frequently got caught in the nets of local Chiba fishermen, so Tateyama resident Kan Shiota proposed to the fisheries cooperative that he would feed the houndsharks to lure them away from the nets. And the plan worked. The sharks now congregate off Ito, where Kan feeds them twice a day. Seeing around 50 of the slender-bodied hunters is not unusual. They’re around 1 to 1.50 m (3 to 5 ft) in length and have a non-aggressive temperament. They politely took mackerel from my gloved hands.

japan diving
Photo by Kan Shiota, Bommie Dive

The feeding also lures other marine life to the site, so you can look forward to an absolute whirlwind scramble of fish, including moray eels, massive red stingrays, higedai and kobudai (whose amazing female-to-male transformation featured in part 1 of Blue Planet II) and two types of large Japanese wrasse. You can also find Japanese bullhead sharks resting in the cracks of the artificial reef around the feeding site and other fish if you want to get away from the action for a bit.

While getting right into the scramble is absolutely exhilarating, the faint of heart can just observe the action from above by holding on to one of the lines that hold the bait cases. The shark scramble is a deep dive, so you must be advanced certified or you can take the deep dive specialty course on the day with Kan, who speaks good English. Bommie dive in Tateyama, Chiba Prefecture is a day-trip dive from Tokyo.

5. Gifu giant Japanese salamanders

japan diving
Photo by Naofumi Ueda of Dive Kooza

My final recommendation is one of the most unique dive experiences you could possibly have. The endemic Japanese giant salamander grows up to 1.5 m (5 ft) and can pass for a docile mini-godzilla. You can rub shoulders with them in the mountain rivers of Gifu and in Koza River in Wakayama Prefecture. The best time to see them is during breeding season when the males, called den masters, are guarding the nests.

Mountain rivers are the epitome of refreshing (read: freezing), meaning you’ll need a drysuit to dive there. It’s still a very off-the-beaten-path dive adventure. For those that don’t speak Japanese, Yoshihiro Ito would be the point of contact as a local guide in Gifu, as he speaks some, but not perfect English: yoseadiv@hyper.ocn.ne.jp. Gifu City is about 2 hours by Shinkansen from Tokyo. If you are in Kansai, go with Dive Kooza in Kushimoto, Wakayama Prefecture. They have an English website and can take you to Koza River. About 3 hours from Osaka.

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