Through histological analyses, this investigation reveals an unusual high incidence of hermaphroditism in Megapitaria squalida, a gonochoric species. A total of 684 specimens were sampled at monthly intervals from February 2007 to January 2008 at Bahía de La Paz and Bahía Magdalena, Baja California Sur, Mexico. Microscopic examination showed that 21.8% of specimens from Bahía de La Paz and 23.5% from Bahía Magdalena were hermaphroditic; in both areas, hermaphroditism was found throughout the year, although in variable proportions. In general, a significantly higher number of females relative to males (chi-square, P < 0.05) were observed in both areas. Our findings indicate that this unusual incidence of hermaphroditism was likely caused by the low population density resulting from overfishing.