This is the first host record of Gymnophallus choledochus metacercariae infecting the polychaete Diopatra neapolitana in the Aveiro estuary (Portugal). The metacercariae were found unencysted, and their morphology is similar to that presented by metacercariae harbored by Nereis diversicolor and Cerastoderma edule, although they are larger in size. In D. neapolitana, the prevalence and mean intensity of the infection was very high, at 100% and 202 ± 139 metacercariae per host, respectively, suggesting that this polychaete is the most suitable host for G. choledochus in the Aveiro estuary. In terms of distribution within the host, the metacercariae were found almost exclusively in the branchial segments (97.4%). This, in conjunction with the close relationship between the mean intensity and branchial surface area, suggests that the branchiae may be the site of entry into the polychaete. Within the branchial segments, the sites selected by the metacercariae are the parapodia (68.9%), where they are mostly located inside the setal sac, and the longitudinal muscles (22.3%), causing hypertrophy and rupture of the muscle bundles, respectively. These histological changes suggest a reduction in polychaete mobility, which should aid the easy predation of infected hosts by birds and thus facilitate the continuity of the G. choledochus life cycle.