To investigate geographic genetic structures and taxonomic relationships among isolated populations of Buergeria japonica, occurring very widely in various habitats of the Ryukyu Archipelago and Taiwan, we conducted phylogenetic and demographic analyses among individuals from various localities, representing their entire distributional ranges. Buergeria japonica is genetically greatly differentiated and comprises three major clades (the Southern Taiwan [ST] clade, the Northern Taiwan Southern Ryukyu [NT/SR] clade, and the Central Northern Ryukyu [CR/NR] clade), each of which seems to represent independent species. The first divergence in the species is estimated to have occurred in the middle to late Miocene in areas of current Taiwan, then eastern periphery of the Asian continent. Split of the ST and the remaining clades, and subsequent divergence between the NT/SR and the CR/NR clades in the latter, indicate consecutive south to north vicariant diversifications. However, these vicariances are not always associated with formation of significant barriers such as deep straits. Less but still prominently diverged subclades (the Amami Tokara [AM/TK] and the Okinawa [ON] subclades) in the CR/NR clade were recognized in spite of the absence of an intervening deep strait. Contrariwise, individuals from Amami and Tokara Groups formed the AM/TK subclade in spite of the presence of the intervening Tokara Gap (a long-standing deep tectonic strait). Furthermore, in the AM/TK subclade, low but definite genetic divergence was found between the Northern Amami Tokara (NAM/TK) lineage and the Southern Amami (SAM) lineage. Estimated divergence time and gene flow rate within the NAM/TK lineage indicate that this species reached northern Tokara from the south by overseas dispersal over the Tokara Gap long after its formation, but not by more recent artificial transportation. This overseas dispersal would have been facilitated by its more frequent occurrence around coastal habitats than other frogs.