Dental morphological differences in the first two mandibular molars of domestic equids have been claimed to possess unique species characteristics and are commonly used to identify archaeological equids to a species level. However, the intraspecific and intra-teeth variability of this morphological trait seems to be largely underestimated and the effects of inter-observer variations are rarely discussed. Therefore, the reliability of such morphological trait is poorly understood. Geometric morphometric (GM) methods can be used to evaluate the level of diversity between different dental morphology and, thus, is a more quantitative and objective approach than visual qualitative observation. This paper aims to examine the intraspecific and intra-teeth variability of lower molar morphology by applying GM analysis on molars from archaeological horses and purported mules as well as modern specimens of known species. The results suggest that other than possible inter-observer variations, the large intraspecific variability deems the dental morphology in lower molars to be unreliable for species identification.