Across its native range, Bull Trout (Salvelinus confluentus) extent and abundance are in decline due to historic overharvest, invasive species and habitat degradation. These factors inhibit Bull Trout recovery and can lead to negative genetic consequences. To establish baseline population genetic understanding of Bull Trout in the Athabasca River Basin, 431 Bull Trout from 20 sites across Alberta’s Eastern slopes were sampled, and compared using 10 microsatellite loci to characterize within- and among-population genetic variation. The Saskatchewan and Athabasca River basins contained similar levels of heterozygosity but were differentiated from one another, suggesting that Bull Trout in the watersheds have similar genetic diversity, but are genetically differentiated from one another. Within the Athabasca River basin, five genetically differentiated clusters were identified. Additionally, no ‘Isolation By Distance’ pattern was found between sites, suggesting that some near populations are genetically differentiated while some distant populations are genetically similar to one another.