The value of craniometrics in classifying brocket deer has been a topic of debate, with its effectiveness within this genus being unclear. This study addressed this uncertainty by examining craniometric data from sympatric species of brocket deer. We present a dataset integrating both published and original data, to elucidate the potential species differentiation by analyzing the inter- and intraspecific variation. Leave-one-out cross-validation (LOOCV) yielded >95% accuracy in species classification. We observed that variation in skull size primarily involves overall size changes rather than specific variation in skull shape among the species. Our findings demonstrate the effectiveness of multivariate craniometric data for taxonomic classifications and offer valuable insights into the evolutionary dynamics of brocket deer species. The observed multidimensional distinction among brocket deer skulls suggests that disruptive selection plays a key role in driving differences in body size across species, while latitude might be an additional important confound factor.