Over 125 years ago, Charles Darwin suggested that the only way to fully understand the form and function of human facial expression was to make comparisons to other species. Nevertheless, it has been only recently that facial expressions in humans and related primate species have been compared using systematic, anatomically-based techniques. Through this approach, large scale evolutionary and phylogenetic analyses of facial expressions, including their homology, can now be addressed. Here, the development of a muscular-based system for measuring facial movement in rhesus macaques (Macaca mulatta) is described based on the well-known FACS (Facial Action Coding System) and ChimpFACS. These systems describe facial movement according to the action of the underlying facial musculature, which is highly conserved across primates. The coding systems are standardized, so their use is comparable across laboratories and study populations. In the development of MaqFACS, several species differences in the facial movement repertoire of rhesus macaques were observed in comparison to chimpanzees and humans, particularly with regard to brow movements, puckering of the lips, and ear movements. These differences do not appear to be the result of constraints imposed by morphological differences in the facial structure of these three species. It is more likely that they reflect unique specializations in the communicative repertoire of each species.