Sulawesi is a biodiversity hotspot for medaka fishes (Adrianichthyidae), with many species endemic to single ancient lakes or lake systems. Frequent vicariance by lake fragmentation since the Pliocene may be largely responsible for diversification in this family. In this study, we demonstrate that not only lacustrine species but also riverine species are also deeply divergent even within a single river system. Phylogenomic and population genetic structure analyses based on genome-wide single nucleotide polymorphisms revealed that a medaka species newly discovered from Cerekang River is sister to Oryzias dopingdopingensis, another riverine species endemic to Doping-doping River. However, the Cerekang Oryzias was clearly separated from O. dopingdopingensis, despite that Cerekang River and Doping-doping River share common estuarine waters. Coalescent-based demographic inference demonstrated that the ancestral population of these two riverine species had experienced a substantial population decrease and subsequently separated into two sub-populations. We infer that the Cerekang Oryzias and O. dopingdopingensis are of lake-origin and are relic species which were left in these rivers after the lake disappeared, and that they have lost their dispersal ability when inhabiting the ancient lake. The lost dispersal ability possibly contributed to the formation of the biodiversity hotspot for this fish group on this island.