The Keramashoto Coral Reef, home to 248 species of reef-building corals, was designated a Ramsar Site in 2005. Around June, the corals spawn, and some of their surviving larvae are swept out 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 contain 46 different tree species, where fan palms and Ryukyu pines grow in abundance. Seasonal winds heavily affect the landscape, so trees grow relatively low to the ground.

The Kerama Islands are home to a variety of unique and rare wildlife, including Sword-tail newt, Ryukyu black-breasted leaf turtle, green sea turtle, Ryukyu robins and Kerama deer. The outlying sea areas of the Kerama Islands are also breeding grounds for humpback whales.