Riverine freshwater fish populations are rarely structuralized within a single river, because their mobility along the river prevents population divergence. Therefore, it is considered to be difficult for population divergence, and much less secondary contact, to occur within a single river system. We found by population structure analyses using genome-wide single nucleotide polymorphisms that two sister riverine ricefishes, Oryzias dopingdopingensis and O. landangiensis, endemic to Doping-doping River and Cerekang River, respectively, in Sulawesi Island, are strongly genetically isolated from each other, despite Cerekang River and Doping-doping River share a connection across estuarine waters. Demographic inference estimated that they diverged about 50,000 years ago. We also found that Oryzias populations recently discovered from downstream Cerekang River are phylogenetically distinct not only from O. dopingdopingensis but also from O. landangiensis. Population structure analyses revealed that gene flows from O. landangiensis to the downstream Cerekang Oryzias have occurred after their secondary contact within Cerekang River, indicating lineage fusion within a single river. Interestingly, these up- and downstream Oryzias have not been completely homogenized. We think that this study is the first that report a freshwater fish group that may have experienced both lineage divergence and lineage fusion within a small single river system.