The mating system of the Mediterranean monk seal was studied combining the use of diverse technologies. Sexual dimorphism in size was limited. Sexual activity was only observed to occur in the water. The different segments of the population segregated spatially: females, pups, and juveniles aggregated inside two main caves, whose entrances were controlled by a small number (2–3) of territorial males that defended aquatic territories situated at the very mouth of the caves. Other territorial males defended aquatic territories located further away (5–30 km). The tenure of aquatic territories was nonseasonal and spanned several years. Relatedness among pups belonging to the same cohort was low or null, indicating a low level of polygyny, which is not surprising for an aquatically mating phocid with a protracted reproductive season. However, in addition, genetic relatedness showed a remarkable temporal periodicity. These results in combination point to the existence of a complex social structure in this species.