The genetic study of animal populations has become a valuable tool in conservation programs, particularly of those species that are endangered. Different population parameters can be determined in both captive and wild animals to assess their genetic status and long-term viability. In Mexico, different genetic tools have been used in the three species of nonhuman primates to assess, reinforce or test different biological aspects that have been determined by observations and field work. Among others, taxonomic and biogeographic aspects, differentiation and population structures, patterns of kinship and social systems have been made to know and understand the biology of the species and direct conservation and survival strategies of the genus Alouatta in Mexico.