Morphological differentiation of island-dwelling organisms provides model systems for studying evolution. Computed tomography (CT) scanning is an entirely non-destructive technique that provides detailed three-dimensional (3D) images of physical structures. Geometric morphometrics has been increasingly used in avian morphology studies by analyzing 3D data obtained from CT scans. We used geometric morphometrics to evaluate the morphological details of the skulls of three, genetically distinct, island populations of the Ryukyu Scops Owl Otus elegans: O. e. elegans from the northern part of the Ryukyu Archipelago, O. e. elegans from the southern part of the Ryukyu Archipelago, and O. e. interpositus from Minami-daito Island. Skulls were scanned using an X-ray CT system and the digitized 3D coordinates of 16 landmarks for each skull were analyzed in order to describe geometric morphometric features. O. e. interpositus was found to have a significantly smaller skull than either population of O. e. elegans. From principle component analysis of shape variation, we also found that the skull shape of O. e. interpositus differed significantly from both the northern and southern groups of O. e. elegans. This difference was in terms of PC1, which mainly represented relative anteroposterior length, and angle of the orbit. We inferred that the small skull of O. e. interpositus is partly a consequence of the particular founders of the population, or evolutionary selection that has taken place on Minami-daito Island and that the distinctive shape of the skull of O. e. interpositus is partly a consequence of adaptations for foraging efficiency, or of morphological integration.