In order to determine the morphological variations of the Japanese swimming crab, Charybdis japonica, we conducted morphological analysis of five populations that are relatively abundant in Korea and Japan. Abdominal sternite for individuals of the Tean population showed significantly short when compared to those of other populations. Principal component analysis demonstrated that morphological differentiation was due to differences (A/Q, B/M, D/P, F/O, J/K), and effectively discriminated each others. The first two components accounted for 40.9% and 60.7% of the variation, respectively. The dendrogram showed three distinct groups, Tokyo population, Taean population, and the other populations.