Biogeographic barriers potentially restrict gene flow but variation in dispersal or vagility can influence the effectiveness of these barriers among different species and produce characteristic patterns of population genetic structure. The objective of this study was to investigate interspecific and intraspecific genetic structure in two closely related species that differ in several life-history characteristics. The grey teal Anas gracilis is geographically widespread throughout Australia with a distribution that crosses several recognized biogeographic barriers. This species has high vagility as its extensive movements track broad-scale patterns in rainfall. In contrast, the closely related chestnut teal A. castanea is endemic to the mesic southeastern and southwestern regions of Australia and is more sedentary. We hypothesized that these differences in life-history characteristics would result in more pronounced population structuring in the chestnut teal. We sequenced five nuclear loci (nuDNA) for 49 grey teal and 23 chestnut teal and compared results to published mitochondrial DNA (mtDNA) sequences. We used analysis of molecular variance to examine population structure, and applied coalescent based approaches to estimate demographic parameters. As predicted, chestnut teal were more strongly structured at both mtDNA and nuDNA (ΦST= 0.163 and 0.054, respectively) than were grey teal (ΦST < 0.0001 for both sets of loci). Surprisingly, a greater proportion of the total genetic variation was partitioned among populations within species (ΦSC= 0.014 and 0.047 for nuDNA and mtDNA, respectively) than between the two species (ΦCT < 0.0001 for both loci). The ‘Isolation with Migration’ coalescent model suggested a late Pleistocene divergence between the taxa, but remarkably, a deeper divergence between the southeastern and southwestern populations of chestnut teal. We conclude that dispersal potential played a prominent role in the structuring of populations within these species and that divergent selection associated with ecology and life history traits likely contributed to rapid and recent speciation in this pair.