In order to describe the resting and pupping habitat of the Critically Endangered Mediterranean monk seal Monachus monachus and facilitate the identification of preferences by the species for suitable habitat for resting and pupping, 94 sea caves in the archipelago of Madeira were located, charted, and categorized using six characteristics. A cluster analysis indicated that there are eight different types of cave, in three groups. Observations of cave usage indicate that monk seals in the archipelago do not appear to exhibit a preference for certain cave types for resting. When taking care of young, however, the species appears to prefer sea caves that have beaches above sea level during high tide and long entrance corridors. Based on these preferences we believe that although there is a large number of caves in the area that are suitable for resting, only 16 (17%) of the caves are suitable for pupping. The survival of the Critically Endangered Mediterranean monk seal will depend on the allocation of sufficient suitable habitat for reproduction.