Although several phylogenetic studies of Gyps species have been conducted, few studies have addressed the genetic diversity of these species on a finer scale such as microsatellite analyses. We collected samples of migratory adults and nestlings from four species of vultures in six different localities. We analyzed the samples using microsatellites in order to determine the genetic distance as well as the amount of variation within and among Gyps species populations. Low genetic diversity in Long-billed Vultures (G. indicus) was probably indicative of a single population with no immigration and low gene flow. As this species is critically endangered, future conservation programs should consider genetically suitable stock for a breeding and reintroduction program. High genetic diversity in African White-backed Vultures (G. africanus) was likely indicative of a number of populations, with immigration and gene flow. We confirmed previous findings of low genetic differentiation among Griffon Vulture (G. fulvus) populations, which indicated high mobility and gene flow among these populations.