The paradise fish, Macropodus opercularis, was once thought to have been introduced to the Ryukyu archipelago from China. However, recent analyses have indicated regional differences in their reproductive characteristics. Therefore, the present study compared the morphological characteristics of the Ryukyuan population with those of continental populations from China and Vietnam by analyzing 27 external characteristics and vertebral morphologies in 10 specimens collected from Okinawa Island. The Ryukyuan population showed significantly deeper and wider heads and shorter caudal fins than those of the continental populations, and local variations were observed in some countable characteristics (lateral line scales, caudal vertebrae, and soft rays on the unpaired fins) among the three populations. These results imply the presence of a cryptic local population of paradise fish.