It has been a central subject in biogeography how geological history has shaped current distribution patterns and population structures of organisms. Sulawesi, an island in the Indo-Australian Archipelago, is known to exhibit characteristic intra-island geographic structuring in many taxa. Here, we report one of the historic vicariant barriers in the island persists in a freshwater fish group even within a single water system. The Malili Lake system is a lake system in central Sulawesi, where five tectonic lakes are connected by rivers and a group of closely-related lacustrine species of medaka (Oryzias) have been reported. Recently, we discovered a phylogenetically-distinct riverine Oryzias from Ussu and Cerekang Rivers, which share the estuary region with Larona River, the only drainage from the lake system. This co-occurrence in the single water system suggests that these phylogenetically-distinct lacustrine and riverine species have a chance to secondarily contact with each other. However, our field surveys revealed no Oryzias inhabits Larona River. Mitochondrial DNA analyses also revealed that the riverine species is isolated from the lacustrine species in spite of water connectivity. Interestingly, population structuring was evident even within the Ussu-Cerekang River system. In the presentation, more detailed population structure analyses using ddRAD-Seq will be introduced.