Speciation can be caused by divergent adaptation in allopatry as a result of ecological or reproductive character displacement in sympatry or parapatry. The latter can result as a means of preventing hybridization, a process known as reinforcement speciation. Though this has been described in a variety of taxonomic systems though the prevalence throughout nature is still unknown. In this study, we use whole-genome sequencing (WGS) of two primate species that have experienced introgression in their history, the rhesus (Macaca mulatta) and cynomolgus (M. fascicularis) macaques, to identify genes exhibiting a pattern of reproductive character displacement consistent with reinforcement speciation. Using windowed scans of various population genetic statistics to identify reproductive character displacement, we find candidate genes associated with a variety of functions, including an overrepresentation of multiple neurological functions and some genes involved in sexual development and gametogenesis. This suggests a variety of genes acting at multiple stages of a reinforcement process between these species. We also find signatures of introgression of the Y-chromosome that confirm previous studies suggesting male-driven introgression of M. mulatta into M. fascicularis populations. This study is among the first to utilize whole-genome sequencing to analyze the phenomenon of reinforcement and among the first to find evidence of this phenomenon in primates, particularly ones that have medical relevance.