The evolution of parental care has been a focal subject in behavioral ecology for decades. Many female medaka fishes (family Adrianichthyidae) deposit eggs on submerged plants or other material and lack parental care. However, at least three medaka species in Sulawesi, an island in the Malay Archipelago, exhibit maternal care: females cover their egg clutches with their extended pelvic fins until they hatch. Sulawesi harbors 16 endemic medaka species, suggesting that they have diverged within the island. However, the phylogeny and reproductive behaviors of the Sulawesian medaka fishes have not been examined comprehensively; therefore, when the pelvic-fin brooding behavior evolved during this diversification is not clear. Field and laboratory observations of 13 Sulawesian medaka fishes revealed that pelvic-fin brooding occurs in at least four species. Molecular phylogenies based on mitochondrial DNA sequences revealed that these four species are separated into two distant clades, suggesting that the unique pelvic-fin brooding behavior evolved independently more than once during the diversification of Sulawesian medaka fishes.