The domestication of the horse – specifically its use as a transport animal – had a unique impact on the evolution of human societies. Along with its influence on warfare, the horse transformed land transportation, radically altering the distance that humans could travel in a day, week, month or lifetime. Over the last century horse domestication has been investigated by zooarchaeologists using morphometric, morphological and (more recently) biomolecular approaches in attempts to identify distinct ‘domestic’ phenotypes in the fossil record. However, identification of domestic morphotypes have been complicated by the low variation in equid cranial morphology and apparent limited changes brought about through the domestication process compared with other domestic taxa. Furthermore, cranial morphology is too prone to ecophenotypic plasticity to provide relevant taxonomic markers. Even dental morphology (of primary importance for taxonomic investigation in the fossil record) has been dismissed as a useful marker for horse domestication, since variations in tooth size and enamel patterns are considered to be too greatly influenced by age and continuous tooth wear. The proof-of-concept study presented here re-evaluates the potential of cheek teeth shape to capture significant differences between horse populations. Using geometric morphometrics (GMM), we study the enamel-folding pattern of the upper P2 and M3, selected for their distinctive morphology amongst the cheek teeth. Curated specimens of known age and sex from two horse (Equus caballus) breeds – Icelandic and Thoroughbred – were used to investigate whether the effects of age (through occlusal wear), sexual dimorphism and allometry (size-related change in shape) should be regarded as confounding factors preventing any accurate discrimination between these two populations. The results show that a landmark based approach applied to the occlusal enamel folding of the P2 and M3 captures significant differences in size (centroïd) and shape between the horses breeds studied. Age-related factors, allometric scaling and sexual dimorphism are not confounding factors in their discrimination, encouraging the use of dental form in population-based research on ancient horse remains.