We used microsatellite DNA to study the population genetics of 4 Alouatta species from Central and South America. Our main findings include the following: (1) A. seniculus had the highest level of microsatellite variability while A. caraya and A. palliata had the lowest mean number of alleles per locus and the lowest expected heterozygosity, respectively; (2) the samples of A. seniculus and A. palliata came from different regions and were not in Hardy-Weinberg equilibrium (HWE) which may indicate a Wahlund effect and differentiated gene pools – in contrast, A. macconnelli and A. caraya were in HWE; (3) the microsatellite genetic heterogeneity of the 4 Alouatta species was similar to the karyotype divergence found among these Alouatta species; the species pair with the lowest level of heterogeneity (genetic differentiation) was A. seniculus/A. caraya , while the Central American species, A. palliata , was highly differentiated from the other 3 South American species; (4) we recommend the establishment of a conservation plan to help protect A. caraya because the Cornuet and Luikart procedure demonstrated a recent bottleneck for this species.