We investigated phylogenetic relationships among Otus scops owls from Socotra Island, the Arabian Peninsula and East Africa using molecular, vocalization and biometric data. The Socotra Scops Owl Otus senegalensis socotranus, currently treated as a subspecies of the African Scops Owl Otus senegalensis, is more closely related to the Oriental Scops Owl Otus sunia and to the endemic Seychelles Scops Owl Otus insularis. Considerable mitochondrial genetic distance and significant morphological differentiation from its two closest relatives, as well as its distinctive vocalizations compared with O. insularis, strongly support recognition of Socotra Scops Owl as a full species. Unexpectedly, two taxa from the Arabian Peninsula, Pallid Scops Owl Otus brucei and African Scops Owl Otus senegalensis pamelae, represent very distinct lineages; O. brucei is basal to a clade that includes taxa found in the Indo-Malayan region and on Indian Ocean islands. In contrast, O. s. pamelae occupies a well-supported basal position within a clade of continental Afro-Palaearctic taxa. The uncorrected-p genetic distance between O. s. pamelae and its closest relatives (other populations of senegalensis from mainland Africa) is c. 4%. As O. s. pamelae is also well differentiated phylogenetically, morphologically and vocally from O. s. senegalensis, we recommend its elevation to species status, as Otus pamelae. Among mainland African O. senegalensis subspecies, Ethiopian populations appear to represent the most divergent lineage, whereas other lineages from Somalia, Kenya and South Africa are poorly differentiated. The large genetic distance between the Ethiopian haplotype and other African haplotypes (3.2%) suggests that the Ethiopian Otus may represent a cryptic taxon, and we recommend that more individuals be sampled to assess the taxonomic status of this population.