There are fifteen autochthonous species within the subfamily Leuciscinae (Cyprinidae) in Spain, all of them endemic except for two. The diversity, peculiarity and complex taxonomic position of most of these species make them an interesting group to study. In the present work, 456 specimens of 11 species were studied. Cleithra, opercular and pharyngeal bones were extracted from each specimen. These bones were compared and measured morphologically to obtain biometric indices. The biometric differences for each bone and for the three bones together were analysed using these indices by means of Principal Component Analyses. The results show a direct relationship between morphological and biometrical differences and similarities. Besides, this osteological comparison partially agrees with the present taxonomic position of these species, contributing to the difficult systematics and phylogeny of this group.