Comparing the patterns of population differentiation among genetic markers with different modes of inheritance can provide insights into patterns of sex-biased dispersal and gene flow. The Blue-and-yellow Macaw (Ara ararauna) is a Neotropical parrot with a broad geographic distribution in South America. However, little is known about the natural history and current status of remaining wild populations, including levels of genetic variability. The progressive decline and possible fragmentation of populations may endanger this species in the near future. We analyzed mitochondrial DNA (mtDNA) control-region sequences and six microsatellite loci of Blue-and-yellow Macaws sampled throughout their geographic range in Brazil to describe population genetic structure, to make inferences about historical demography and dispersal behavior, and to provide insight for conservation efforts. Analyses of population genetic structure based on mtDNA showed evidence of two major populations in western and eastern Brazil that share a few lowfrequency haplotypes. This phylogeographic pattern seems to have originated by the historical isolation of Blue-and-yellow Macaw populations ∼374,000 years ago and has been maintained by restricted gene flow and female philopatry. By contrast, variation in biparentally inherited microsatellites was not structured geographically. Male-biased dispersal and female philopatry best explain the different patterns observed in these two markers. Because females disperse less than males, the two regional populations with well-differentiated mtDNA haplogroups should be considered two different management units for conservation purposes.