In Canada, subspecies of the yellow-pine chipmunk (Neotamias amoenus luteiventris) and red-tailed chipmunk (Neotamias ruficaudus ruficaudus) co-occur in a small area of the Rocky Mountains in southwestern Alberta and southeastern British Columbia. Some N. a. luteiventris individuals in this area are of hybrid ancestry, carrying a mitochondrial DNA gene of N. r. ruficaudus. We tested for phenotypic hybridization by comparing genital bone morphology, body size, cranial mandibular morphology, and tail color of mitochondrial hybrids with specimens of the 2 parental reference groups identified from genetics or genital morphology. Hybrids were indistinguishable from the N. a. luteiventris reference group, demonstrating no intermediacy or increased variability. Our results are consistent with genetic data that suggest minimal nuclear gene flow between the 2 taxa. Five hybrid locations were within the contact zone, but 6 were 14–98 km beyond the known range extent of N. r. ruficaudus. These peripheral occurrences may be a legacy of a past range decline of N. r. ruficaudus in response to Holocene climatic changes that left hybrids outside the present-day contact zone. We recommend more field research in the Canadian Rocky Mountains to determine the full range extent of N. r. ruficaudus and N. a. luteiventris of hybrid ancestry.