Arctic Grayling Thymallus arcticus are a salmonid with a Holarctic distribution, extending from northeastern Eurasia through northwestern North America. Throughout their range, Arctic Grayling face a number of threats, including angling mortality, habitat fragmentation and loss, and climate change. Thus, there is a need to protect the species through targeted management actions. Genetic information can assist in determining the appropriate scale for these actions through the description of designatable units. Here we use newly collected mitochondrial DNA sequence data to assess the phylogeographic structure of Arctic Grayling in Alberta, Canada, and link these with previously collected mitochondrial and microsatellite data to determine how many designatable units may exist across Canada. Our assessment of 831 base pairs of sequence data in 96 individuals found two deeply divergent lineages in Alberta. When combined with 22 previously collected sequences, our results highlight that Alberta is a contact zone for the observed lineages of Arctic Grayling in North America. A reassessment of nine microsatellites that were genotyped in 1,116 individuals further highlighted interbasin divergence, likely the result of historical processes. Given the divergence and geographic distribution of the genetic diversity, Arctic Grayling in Canada merit consideration for separate designatable units in future species status assessments and management plans. Continuing research should attempt to expand sampling geographically (e.g., regions east of Great Slave Lake and along the Arctic coastline) to clarify possible colonization routes and add to or synthesize the work on Arctic Grayling behavior, morphology, and life history to address the limited understanding of local adaptions within this species.