Sea cucumbers are a diverse group of echinoderms, approximately more than 1,400 species around the world belonging to six orders and 25 families. In Egypt, sea cucumber is overfished along the Egyptian coast of the Red Sea and in most cases, species are being commercialized without a clear taxonomic identification. Two color morphs of the holothurian Actinopyga mauritiana were found in the Egyptian Red Sea coast and Gulf of Aqaba. Both morphs were found to have different habitats and depth preferences, morphological and molecular examination of both morphs along the Egyptian coast of the Red Sea uncovered new species diversity within the Actinopyga species complex and the discovery of novel species Actinopyga sp. nov.