Rhizocephalan barnacles (Thecostraca: Cirripedia) are parasitic crustaceans that lack appendages, segmentation, and a digestive system in adults, while instead infiltrating their hosts with a nutrient-absorbing system of rootlets. Sacculinids, belonging to the Rhizocephala order, are known for their various parasitization-induced effects on their decapod hosts, such as parasitic castration, reduction in the growth of secondary sexual characteristics, feminization of male crabs, and alteration of host behavior. In this study, we conducted field surveys in Japan at Manazuru Town (Kanagawa) on the Pacific coast, and on Sado Island and Noto Peninsula on the Sea of Japan side, and found that sacculinid-parasite-ratios on the grapsid crab Pachygrapsus crassipes were particularly high on the Sea of Japan coast. Molecular phylogenetic analysis revealed that the Manazuru population forms a single clade with Sacculina yatsui, and both Sado and Noto populations form a single clade with S. confragosa. We further demonstrated that external morphologies of male P. crassipes parasitized by sacculinids were changed to female phenotypes. This host-parasite interaction will be a useful model for understanding molecular mechanisms underlying rhizocephalan-driven morphological and behavioral feminization and castration.