The Eastern Spot-billed Duck (Anas zonorhyncha) historically was rare in the southern Russian Far East. However, during the last 60–70 years, its breeding range in East Asia has expanded northwest; Eastern Spot-billed Ducks are breeding increasingly within the range of Mallards (A. platyrhynchos). We collected 120 Eastern Spot-billed Ducks and Mallards from Primorye, Russia, and sequenced 666–667 base pairs (bp) of the maternally inherited mitochondrial DNA (mtDNA) control region and 255 bp of the ornithine decarboxylase intron six (ODC6). Control region and ODC-6 allele sequences revealed two divergent groups of haplotypes and alleles that differ by 1.5% and 2.0%, respectively, and correspond to Avise et al.'s (1990) group A and B mtDNA haplotypes. Group A mtDNA haplotypes occurred in 22 Eastern Spot-billed Ducks and 78 Asian Mallards, and group B haplotypes occurred in 14 Eastern Spot-billed Ducks and 4 Asian Mallards. Moreover, the group B haplotypes that we observed predominantly in Eastern Spot-billed Ducks (i.e. group SB) were monophyletic and diverged by 2–16 substitutions from group B haplotypes previously sequenced from 241 Mottled (A. fulvigula), American Black (A. rubripes), and Mexican ducks (A. diazi), and from North American Mallards. In contrast, type 1 and 2 ODC-6 allele frequencies for Eastern Spot-billed Ducks and Mallards did not differ, but heterozygosity for the former was greater than expected under Hardy-Weinberg equilibrium. Our analysis is the first to document the existence of two divergent haplotype and allele lineages (group A and B, type 1 and 2) in Asian mallard species and suggests that Eastern Spot-billed Ducks are more closely related to North America's Mottled, American Black, and Mexican ducks than they are to Mallards, which occur sympatrically in East Asia. Our data are consistent with the hypothesis that Eastern Spot-billed Ducks and Mallards have hybridized extensively in the Russian Far East. If so, apparent differences in group A and B mtDNA haplotype ratios, effective populations sizes, and migration rates indicate that many more male Eastern Spot-billed Ducks mated with female Mallards and more Eastern Spot-billed Ducks received ODC-6 alleles from Mallards than vice versa. We hypothesize that those differences reflect strong female natal-site fidelity and high levels of male dispersal, and that Mallards significantly outnumber Eastern Spotbilled Ducks in Primorye. Excess heterozygosity in Eastern Spot-billed Ducks (and in Mallards to a lesser extent) is probably maintained by ongoing emigration of Eastern Spot-billed Ducks and Mallards from areas of allopatry outside the Primorye region, where Eastern Spot-billed Ducks and Mallards are predicted to possesses genotypic frequencies historically diagnostic of each species.