The prevalence of parasites in gonads of the clam Megapitaria squalida (Sowerby, 1835) was investigated at Santa Rosalía mining port in the Gulf of California. A total of 696 gonads were histologically analyzed, observing an unusual parasitic castration caused by the development of trematode larvae within follicles. Trematode sporocysts within follicles containing germinal balls and developing cercariae were observed and associated with an inflammatory response, as evidenced by a heavy hemocytic infiltration and the formation of granulocytomas surrounding the parasite structures. Some metacercariae were observed within ovarian connective tissues suggesting that M. squalida could also act as a second intermediate host for digenean trematodes. Infection was age specific as juvenile clams (1-4-cm shell length) did not contain parasites and prevalence in the adult clams increased with size. Unlike males, which presented four levels of infection density, all the parasitized ovaries of females showed very high infection densities. The prevalence was significantly (χ² = 6.99; df = 1; P = 0.001) higher in females (30.2%) than in males (17%). The highest prevalence of parasitized clams was in the ripe stage during the summer (43.7%) when seawater temperatures were highest, whereas the lowest prevalences were observed in winter. It is possible that the polluted environment of Santa Rosalía could increase the occurrence and high infection density by trematode larvae in M. squalida.