A new tellinid species, Pharaonella amanyu sp. n., is described from sand banks around Amami Islands, the Ryukyu Archipelago, in southern Japan. A molecular phylogenetic analysis suggests that this new species is closely related to P. sieboldii. This species has long siphons and lives buried deep in well-sorted white sand syntopically with Tonganaella tongana. These rare, large tellinid species are indicators of unspoiled tidal/subtidal sand flats, which should receive the highest priority conservation in the Ryukyu Archipelago.