Alternative alleles at a locus on the W chromosome of Papilio glaucus (causing dark or yellow wing colors, respectively) underlie a female-limited mimicry polymorphism thought to be maintained by balancing selection. In species with heterogametic females (i.e., the ZZ-male/ZW-female sex chromosome system), the mitochondrial DNA and the W chromosome are genetically linked because they are both maternally transmitted. We investigate the association of COI and COII mitochondrial DNA haplotypes with alternative W-linked phenotypes. Surprisingly, we find no congruence between mitochondrial DNA genealogies and inferred W-linked color alleles in P. glaucus. Using a maximum-likelihood phylogenetic approach, we reject the hypothesis of monophyly for dark-morph mitochondrial DNA lineages, even in the presence of putative low-frequency mimicry suppressor alleles or alternative melanizing factors. The most likely genealogical tree topologies assume more than one exchange event between mitochondrial DNA cytotype and the W-linked color morph. These results suggest that there is either paternal leakage of mitochondrial DNA or that more than two W-linked alleles underlie the alternative color morphs. Using data from an additional mitochondrial DNA locus, ND5, we show that pairwise linkage disequilibrium decays with physical distance between polymorphic sites. This finding suggests that genetic exchanges between maternal and paternal mitochondrial DNAs may have contributed to the lack of association we observe between phenotype and genotype.