|Speciation and hybridization drive all of the biodiversity seen on the plant. Understanding underlying mechanisms of these cornerstones of evolutionary genetics if of vital importance. Here we seek to apply a combination of in silica methods to characterize at the genomic level a group of hybridizing macaques broadly distributed across southeast Asia. Using a mixture of structural variation programs and population genetics we aimed to better understand this system. Here we establish the need to run multiple variant detection programs and intersect the outputs to attain a high quality variant list. Additionally, evidence was found supporting faster X evolution in these two macaques. Finally, rates of variation and divergence were found to overlap more often than by chance at a rate of 81%. This research can provide a vast foundation for further research into primate evolution and macaque genomics and genetics.