Mitochondrial-DNA (mtDNA) variation in Rocky Mountain bighorn sheep was assessed to determine relationships among populations and the usefulness of mtDNA analysis for the conservation of bighorn sheep. Phylogeographic analysis revealed relatively divergent mtDNA haplotypes within herds and several geographically widespread haplotypes. This suggested that gene flow has occurred on a regional scale at some time in the past and that populations have not been subdivided by long-term biogeographic barriers. Nonetheless, significant differentiation in mtDNA-haplotype frequencies among herds suggested that little gene flow currently exists among populations. Failure to recognize that historical (phylogeographic) and current population structure may not be concordant could lead to erroneous conclusions and conservation strategies.