The warm Kuroshio Current runs offshore, and sustains coral reefs and the northernmost mangroves in the western Pacific.

The dominant trees are Castanopsis sieboldii, Quercus miyagii, Persea thunbergii, and Schima wallichii ssp.

In the mountain forests of Yakushima Island, conifers including Cryptomeria japonica, Chamaecyparis obtusa, Tsuga sieboldii, and Abies firma, are mixed with the broadleaf evergreen trees above 1200 meters elevation.

Mangrove species include Bruguiera gymnorhiza, Heritiera littoralis, Rhizophora stylosa, Avicennia marina, Sonneratia alba, and Nypa fruticans.

The Ryukyu minivet (Pericrocotus tegimae) is formerly endemic, but in recent decades has spread to Kyushu, Shikoku, and western Honshu.