A detailed study of the gonads of two endangered species of the genus Margaritifera living in the Iberian Peninsula, Margaritifera auricularia (Spengler, 1793) and Margaritifera margaritifera (Linnaeus 1758), based on macroscopic and histological observations is presented. In both species, gonadal tissue occurs within the visceral mass without a specific location. In hermaphrodite specimens, male and female acini are mixed in the visceral mass but can be clearly distinguished by detailed macroscopic study. The gonadal topography and cycle of Margaritifera auricularia is described for the first time, indicating that the species is a female hermaphrodite and that gametogenesis occurs from December to March. Fifty percent of Margaritifera margaritifera specimens studied were hermaphrodites and 50% females.