The age, total length (LT), head shape and skull shape were investigated for 379 Japanese eels Anguilla japonica sampled in freshwater and brackish areas of the Kojima Bay–Asahi River system, Okayama, Japan, to learn about the differentiation process of head-shape polymorphism. The relative mouth width (ratio of mouth width to LT) of A. japonica > 400 mm LT collected in fresh water was significantly greater than that of fish collected in brackish water. Growth rates of mouth width and the distance from the snout to the midpoint of the eyes (the ratio of width and distance to age, respectively) were not significantly different between freshwater and brackish-water samples, whereas the somatic growth rate (the ratio of LT to age) of freshwater samples was significantly lower than that of brackish-water eel samples. These results suggest that the factors affecting head and somatic growth of A. japonica are not identical. According to these results and feeding patterns in each habitat reported by another study, it is suggested that somatic growth appears to play a significant role in the differentiation process of the head-shape polymorphism in A. japonica, with the slow-growing fish in fresh water becoming broad-headed and the fast-growing fish in brackish water becoming narrow-headed.