In mammals, fine motor control is essential for skilled behavior, and is subserved by specialized subdivisions of the primary motor cortex (M1) and other components of the brain’s motor circuitry. We profiled the epigenomic state of several components of the Rhesus macaque motor system, including subdivisions of M1 corresponding to hand and orofacial control. We compared this to open chromatin data from M1 in rat, mouse, and human. We found broad similarities as well as unique specializations in open chromatin regions (OCRs) between M1 subdivisions and other brain regions, as well as species- and lineage-specific differences reflecting their evolutionary histories. By distinguishing shared mammalian M1 OCRs from primate- and human-specific specializations, we highlight gene regulatory programs that could subserve the evolution of skilled motor behaviors such as speech and tool use. Further, in order to predict candidate enhancers in additional species for which primary data was not available, we developed machine learning models trained on genome sequence across species. Overall design: To supplement publicly available open chromatin datasets, we generated bulk tissue ATAC-seq data from fresh mouse liver tissue (one male and one female replicate), fresh rat tissues (two male and one female replicate), and fresh macaque tissue (one male and one female replicate). Our data includes cortex, striatum, and liver from all three species, and the cortex and striatum data from macaque consists of multiple sub-regions of these brain regions.