Wolves from the Great Lakes area were historically decimated due to habitat loss and predator control programmes. Under the protection of the US Endangered Species Act, the population has rebounded to approximately 3000 individuals. We show that the pre-recovery population was dominated by mitochondrial DNA haplotypes from an endemic American wolf referred to here as the Great Lakes wolf. In contrast, the recent population is admixed, and probably derives also from the grey wolf (Canis lupus) of Old World origin and the coyote (Canis latrans). Consequently, the pre-recovery population has not been restored, casting doubt on delisting actions.