Divergent selection can lead to substantial morphological and behavioral differences despite slight differentiation in neutral genetic variation. We examined the evolutionary history of two closely related waterfowl, the Cinnamon Teal (Anas cyanoptera) and Blue-winged Teal (A. discors), that are morphologically distinct but paraphyletic in mitochondrial DNA (mtDNA) and share allozyme alleles. Sequences of mtDNA and two nuclear introns revealed that North American Cinnamon Teal (n = 70) and Blue-winged Teal (n = 76) are characterized by high genetic diversity, a large effective population size, and recent population expansion. In contrast, South American Cinnamon Teal (n = 102) have less genetic diversity and a smaller effective population size that has been more stable. We found 91 unique mtDNA haplotypes, only a few of which were shared by the two species or the three subspecies of the Cinnamon Teal, but the haplotypes were intermixed in a polyphyletic relationship, and we found no diagnostic phylogroups. Moreover, populations were more strongly differentiated in mtDNA (Φ_ST = 0.41) than in the nuclear introns (Φ_ST = 0.04–0.06). Analyses of isolation with migration indicated that sharing of haplotypes and alleles in the two continents is more likely attributable to incomplete lineage sorting than to gene flow, whereas estimates within each continent yielded higher migration rates. The oldest divergence was between North American Cinnamon Teal and the other taxa, whereas the Blue-winged Teal likely split from South American Cinnamon Teal more recently. Considerable overlap in confidence intervals for these divergences, however, suggests that these taxa diversified rapidly.