Résumé
Despite their distinct bio-cultural histories, the morphological similarity of sheep and goats complicates their identification in archaeological contexts and limits within-species analyses. Skull remains are still poorly studied, and the inner ear has only recently gained attention in bioarchaeology as the petrous bone encapsulating it preserves DNA well. We applied three-dimensional geometric morphometrics to analyse skull and its parts (occipital, maxilla and frontal bones), including the inner ear, size and shape variation in 26 sheep (six breeds) and 15 goats (three breeds). Shape-based analyses achieved good to perfect species discrimination for all structures analysed (whole skull and inner ears: 100%; parts of the skull: 72–100%), whereas size-based discrimination performed lower (whole skull: 85.2%; inner ears: 86.5%; and parts of the skull: 72–89.9%). Among breeds, variation in size and shape was detected, offering promising potential for tracking domestic populations in archaeological contexts. Although the results showed little correlation between inner ear and skull morphometrics, the orientation of the inner ear in the skull differed between the two species. Our study highlights micro-computed tomography scanning and geometric morphometrics as powerful, non-destructive tools for species identification, complementing ancient DNA analysis and enhancing bioarchaeological research on domestication, husbandry practices and the long-term history of human–animal interactions.