Deeply divergent freshwater fish species within a single river system in central Sulawesi

•We discovered a ricefish species from a river in central Sulawesi.•This river shares estuarine waters with another river where its sister species occurs.•These two species are genetically isolated despite freshwater drainage connectivity.•Coalescent-based demographic inference demonstrated that they are of lake-origin.•They are probably relic species left in these rivers due to lost dispersal ability.