Tokyo Metropolis is one of the 47 prefectures of Japan and has served as the Japanese capital since 1869. Unlike the urban jungle image Tokyo is actually full of nature. It forms part of the Kanto region on the southeastern side of Japan's main island, Honshu, and includes the Izu Islands and Ogasawara Islands. Especially the Islands chains is not easy to access and the inhabitants are small in numbers.
The Izu Islands are a group of volcanic islands and is part of the Fuji-Hakone-Izu National Park. The islands in order from closest to Tokyo are Izu Oshima, Toshima, Niijima, Shikinejima, Kozushima, Miyakejima, Mikurajima, Hachijojima, and Aogashima. This Island is further connected to the Ogasawara Island chain, which is called the Galapagos of Asia.
Diving in Tokyo means diving in these Islands. The Islands are directly in the path of the warm Black currents path bringing in many tropical marine life from the south, and large school of fishes. At Oshima Island, you may encounter large school of Hammerhead sharks. The number of endemic species of animal life you see here in these Islands are also a treat.
Why not enjoy the modern Tokyo and then hop on a ferry or even fly down (you can only fly down to Hachioji jima Island) south to enjoy the untouched nature on your visit to Japan?