In Kanagawa Prefecture and its surrounding area, two types of body color populations (DA: dark and BL: blue) of Japanese freshwater crab, Geothelphusa dehaani, are distributed parapatrically, suggesting some extent of genetic differentiation between them. In this study we examined the genetic variation of G. dehaani in Kanagawa Prefecture and Tokyo by means of electrophoretic analysis on 5 enzyme loci. The results clearly show the existence of substantial genetic differentiation among different color type populations. In addition, some extent of differentiation is also observed within the BL populations.