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The northern flicker is a common woodpecker that inhabits open woodlands throughout North America. A narrow hybrid zone occurs along the range boundaries between the eastern yellow-shafted and western red-shafted subspecies. Mitochondrial DNA (mtDNA) was isolated from 201 flickers from 27 locales, primarily along two transects that cross the hybrid zone, one across the northern United States and one across the southern United States. Analysis of restriction-fragment patterns revealed substantial mtDNA polymorphism. Three restriction endonucleases-HindIII, PvuII, and AvaI-together define eight haplotypes. Geographic variation in haplotype frequencies is highly significant. UPGMA analysis of haplotype frequencies reveals two major clusters of populations, a northern-and-eastern cluster and a southwestern cluster; 86% of the variance in haplotype frequency occurs between the two clusters. Geographic variation in haplotype frequencies is not clearly associated with the hybrid zone. This pattern of divergence may reflect a history of isolation of southwestern populations; alternatively, it is possible that the group of related southwestern haplotypes is adapted to hot, arid conditions common in the deserts of the American Southwest. The gilded flicker is a third subspecies that occurs in the Sonoran Desert. Gilded flickers from Arizona have an mtDNA haplotype closely related to the haplotypes observed in red-shafted flickers of the Southwest.