The Nansei Islands in the southern Japanese Archipelago have 15 taxa of seagrasses from seven genera within three families. Seagrasses in this region grow on coral sands or coral debris in shallow reefs and on sandy or muddy substrata in the shallow areas of bays and inlets. Certain Halophila species grow in deep water off some islands. Enhalus acoroides only reaches to Ishigaki I. with winter sea water temperature (WST) at 23 degrees C, while Okinawa I. (WST at 21.6 degrees C) is the northern biogeographic limit for Halophila decipiens, H. okinawensis, H. major and H. gaudichaudii. Amami-oshima I. (WST at 20.7 degrees C) is the northern border for Thalassia hemprichii, H. minor, H. ovalis, Cymodocea serrulata, Cymodocea rotundata, Syringodium isoetifolium, Halodule uninervis and Halodule pinifolia. Halophila mikii the sole seagrass collected from Yakushima I. (WST at 19.3 degrees C), is of volcanic origin. The distribution of tropical seagrasses in the Nansei Islands is clearly associated with the warm Kuroshio Current, WST and habitat availability. Zostera japonica is the only temperate species occurring in the region. Meadows of Z. japonica, H. ovalis and Halodule pinifolia have disappeared from certain localities in the Archipelago, due probably to human activities and natural siltation.