This study compared aggressiveness between two distinct wild populations of Japanese medaka: a Northern population, Oryzias sakaizumii, and a Southern population, O. latipes. When four males competed in intra-population contests, the social hierarchy was determined based on aggressive acts in both populations. Dominants of the Southern population showed higher aggressive acts than did dominants of the Northern population. Increased aggressiveness of Southern males compared with Northern males was also observed when a pair of Northern and Southern males were compared in inter-population contests. High expression of arginine vasotocin (AVT) in distinct preoptic regions were found in dominants and subordinates of the Southern population, but not in those of the Northern population. In contrast, neither 11-ketotestosterone nor cortisol levels in plasma differed between dominants and subordinates of either population, nor between pairs of the Northern and the Southern males. Taken together, these findings indicate that the two wild populations of medaka represent intriguing models for the study of neuroendocrinological correlates in behavioral traits underlying congeners of medaka fish.