Certain parasites can manipulate their hosts to enhance their own fitness and transmission success. Rhizocephalan barnacles are a notable example, inducing significant changes in their crustacean host's morphology, physiology, and behaviour. Until recently, it was believed that the spider crab Scyra aff. ferox is parasitized by a single species Sacculina pilosella in the Sea of Japan. However, previous molecular studies have revealed a complex of unrelated species, Sacculina pugettiae (fam. Sacculinidae) and Parasacculina pilosella (fam. Polyascidae). These rhizocephalans can even parasitize one host specimen simultaneously. Here, we investigated the interaction of S. pugettiae and P. pilosella with the nervous system of their common host. Species were identified based on receptacle morphology, with further validation through 18S gene phylogenetic analysis. The parasites interacted differently with the host nervous system: S. pugettiae had goblet‐shaped organs in the ganglion periphery, while P. pilosella lacked these structures, instead possessing numerous neuropil rootlets. In case of simultaneous infection, both goblet‐shaped organs and neuropil rootlets were present. Histochemistry revealed the presence of muscular rosettes in the rootlets of both species, suggesting a similar organization of the muscular system despite phylogenetic differences. Scanning electron microscopy confirmed the presence of host cell projections enveloping the rootlets. This study provides insights into the morphological features of rhizocephalan‐decapod interaction and highlights differences in their interaction with host nervous tissue between families. Our results also confirmed the loss of the goblet‐shaped organs in Polyascidae.