The pen shell fishery in northwest Mexico is based on reproductive quota, but the reproductive biology of Pinna rugosa, an economically valuable species, has not yet been documented in its main fishery area. The aim of this study was to evaluate the reproductive cycle of P. rugosa, determine the prevalence of atresia and hermaphroditism, and estimate the effect of environmental variables on its reproduction during 2015. Atresia is part of the reproductive cycle in which the cells undergo degeneration. It generally occurs after spawning to reabsorb compounds but it can also occur from the early stages of gametogenesis, affecting fertilization and recruitment. Gonad samples and environmental parameters were collected monthly from a commercial bank at Laguna Ojo de Liebre (Baja California Sur, Mexico) from January to December 2015. Shell height, sex, gonadal development stages, and atresia prevalence were recorded. The results showed that 14% of the individuals were females, 19% were males, and 67% were hermaphrodites, with 3 forms of functional hermaphroditism. Gonadal inactivity occurred in January, February, November, and December, coinciding with lower temperatures and higher chlorophyll a concentrations. Most individuals spawned in June and July. Calculation of a monthly gonad index revealed that gonad development was positively related to environmental variables (R2 = 0.54). Atresia was observed from March to October and was positively related to environmental conditions (R2 = 0.81). The high prevalence of atresia during periods of high temperature and food scarcity suggests that these environmental parameters can affect the reproductive activity of P. rugosa, and have recruitment and fishery productivity implications.