The recent spread and intensification of Haplosporidium nelsoni (MSX) disease in oysters, Crassostrea virginica, along the Atlantic coast of the United States has heightened interest in the use of disease-resistant strains in aquaculture and increased the need for understanding all facets of how selective breeding affects oyster performance, including reproduction. Resistance does not prevent infection, but involves an ability to restrict parasite development and to tolerate infections. We examined selected and unselected oysters, from three geographical locations, all exposed to H. nelsoni infection, to determine the influence of selection, strain origin, and parasitism on gametogenesis. Gonadal development was most frequently correlated with geographic origin of oysters: northern strains (from Long Island Sound) ripened and spawned earlier than southern strains (from the James River), even after several generations of selection at a single location in Delaware Bay. Parasitism was associated with impaired gonadal development in May when gametogenesis was occurring, but not in August, when spawning was underway. Selection for disease resistance was associated with improved gametogenic development, but only in oysters with few or no patent infections. Both parasite burden and selection for resistance were correlated with gametogenesis only in strains from the two southern-most locations, the James River and Delaware Bay, and never in those from Long Island Sound. We suggest that our observations resulted from interference by H. nelsoni in energy acquisition, storage, and conversion cycles of the oyster, which, in turn, differed seasonally according to geographic origin. Gonad development appeared to be more sensitive to parasitism when gametes were in the formative stage rather than after they had matured. Thus, southern strains, which were still in the early stages of gametogenesis when they experienced typical high parasite loads in late May, showed significantly greater inhibition than northern strains, which already had well-developed gonads at the same time. In contrast to most reports that environmental stress correlates with an increased ratio of males to females, we found a three-fold increase in the proportion of females among H. nelsoni-infected oysters compared to uninfected oysters. There was no evidence of sex-associated differential infection or mortality rates and we suggest that parasitism inhibits the development of male gametes more than female gametes.