Buergeria japonica, long thought to be a single species widely occurring on the Ryukyu Archipelago and Taiwan, proved to include three genetically differentiated clades, (1) the Northern and Central Ryukyu, (2) the Southern Ryukyu and Northern Taiwan, and (3) the Southern Taiwan clades. The Southern Taiwan clade has already been split from the others as a distinct species. A distinct heterospecific relationship of the Southern Ryukyu and Northern Taiwan clade from the Northern and Central Ryukyu clade was also clear from genetic evidence. Morphological comparison between specimens from the Yaeyama (the Southern Ryukyu and Northern Taiwan clade) and Amamioshima, the type locality of B. japonica (the Northern and Central Ryukyu clade), confirmed genetic differences and corroborate their independent species status. Thus, we describe the Northern Taiwan and Southern Ryukyu clade as B. choui sp. nov.