The ricefishes are highly diversified on the Indonesian island of Sulawesi. The scarcity of competing freshwater fish taxa because of the geological isolation may have offered ecological opportunities to ricefishes. Three species of Oryzias ricefish are distributed in Lake Poso, a Sulawesian ancient lake. They are inferred to have speciated in sympatry within the lake. The ecological and reproductive traits divergent between the species could have contributed to the reproductive isolation. Historical introgression from another species in a separate lake is also suggested. However, the genetic bases and evolutionary mechanisms of Lake Poso ricefish speciation remain unknown, including the evolutionary sources of the genetic variation that enabled the speciation. We conduct population genomic and quantitative genetic analyses to reveal the evolutionary mechanisms of ricefish sympatric speciation. We report the genomic divergence and gene flow between the ricefishes and discuss historical introgression between the species that fuelled the genetic variation of the populations and possible traces of natural selection that acted on the species. We also conduct quantitative trait locus analyses to identify genomic regions related to the phenotypic differences between the species, the evolution of which may have been the requisite for the speciation.