The populations of a frog long identified as Fejervarya limnocharis from the Southern Ryukyus (=Sakishima in conventional regional name), Japan, considerably differ genetically and morphologically from the topotypic population of the species from Java. These Southern Ryukyu populations are therefore judged to represent a distinct biological species, which is described here as Fejervarya sakishimensis. This new species differs from F. limnocharis in larger snout-vent length (SVL). Also, it is distinguished from the latter in shorter head and tibia, smaller eye and narrower internarial space, all relative to SVL, and larger ratio of the first toe length to the inner metatarsal tubercle. From F. multistriata, F. sakishimensis differs by relatively larger tympanum, wider head, upper eyelid and anterior and posterior spaces of eyes, and longer forelimb and first toe, besides larger SVL. Furthermore, F. sakishimensis has a larger body, and relatively shorter head, tibia and hindlimb than F. iskandari. Also, this species is differentiated from all other nominate taxa of the F. limnocharis complex by a combination of some morphological characteristics.