The Ryukyu Robin species complex, including the Ryukyu Robin Larvivora komadori and the Okinawa Robin L. namiyei, is endemic to the islands of the Ryukyu Archipelago. Population genetic structure and gene flow within this complex were investigated using 14 nuclear microsatellite markers. Distinct genetic differentiation was detected between the Ryukyu and Okinawa robins, and the Ryukyu Robin was further differentiated into four regional groups belonging to the Danjo Islands, Tokara Islands, Oh-shima with some adjacent islands, and Tokuno-shima. Contemporary gene flow among these regional groups was restricted overall, but outflow from the Tokara Islands group to the other three groups was exceptionally high. This asymmetric pattern may have been affected by differences in the isolation distance, migratory habits, and population size. The Ryukyu Robin species complex was long considered a single polytypic species; however, it has recently been classified as two independent species, mainly owing to the deep mitochondrial DNA divergence between them and a phenotypical re-examination. The genetic structure inferred from the nuclear loci strongly supports their genetic independence. The Okinawa Robin provides the first case among birds for which the splitting of sister species both endemic to the Ryukyu Archipelago is supported by all of the morphological, behavioral, ecological, and genetic evidence. Such recognition appears preferable in avian conservation and biogeography studies. Currently, the Ryukyu Archipelago includes an Endemic Bird Area and two Natural World Heritage sites, making the reliable delimitation of endemic species all the more important. Comprehensive genetic investigation, together with phenotypical re-examination is necessary, even for closely resembling but allopatric sister forms in this region.