The seas around the Kerama Islands are home to 248 species of reef-building corals, and were designated a Ramsar site in 2005. Around June, the corals spawn, and some of their surviving larvae are swept out to make their way to the west coast of the main island of Okinawa and settle in the waters there.
Over 620 native plant species grow in the Kerama Islands. The forests have a variety of 46 tree species, where fan palm and Pinus luchuensis (Ryukyu pine) grow in abundance. The landscape is heavily effected by seasonal winds, so trees grow relatively low to the ground.
The islands have rare wildlife, including Sword-tail newt (Cynops ensicauda), Ryukyu black-breasted leaf turtle (Geoemyda japonica), green sea turtle (Chelonia mydas), Ryukyu robins and Kerama deer. The outlying sea areas of the Kerama Islands are also breeding grounds for humpback whales.