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Within-species, biodiversity can be organized in units, ranging from subspecies to evolutionarily significant units (ESUs), populations and social groups. To define ESUs, researchers often focus on the concordant distribution of traits that exhibit likely adaptive significance, including genetic and ecological variation. Caribou is a Species at Risk in Canada, and are conserved at the level of both subspecies and designatable units (DUs), which are conceptually similar to ESUs. However, the use of genomics has been suggested to provide better delineation of units that are based upon variation of genes—not just neutral genetic markers. Here, we analyzed single nucleotide polymorphisms (SNPs) for 190 caribou belonging to two recognized subspecies and four DUs found throughout western Canada. We confirmed two major genetic clusters, which we refer to as the Northern Caribou and Southern Caribou, characterized by divergence at numerous SNPs and genes with known functions in other mammals. Notably, the distribution of these two clusters did not fully overlap with currently recognized subspecies. A discrepancy with current classification was detected for Mountain DUs, which were thought to belong to the Woodland subspecies, but with significant northern-type ecological traits described in the literature, indicating more work is needed to refine our understanding of this transitional zone. We also detected genetic signals of male-biased dispersal, which may be natural or affected by habitat fragmentation effects on females. This work illustrates the value of genomics in rethinking subspecies and conservation unit designations and better conserve biodiversity within terrestrial species at risk.