Background <p>Ecotypes hold unique behavioral and/or life history diversity. Identifying genetic divergence among ecotypes is critical for informing their designations and conservation status. However, detecting these differences can be challenging, particularly for ecotypes that are rooted in behavior, share habitats, and exhibit high gene flow. In Ontario and Quebec (Canada), two ecotypes of woodland caribou (<i>Rangifer tarandus caribou</i>) with overlapping distributions in winter are recognized: eastern migratory and boreal caribou are morphologically similar yet are distinguished by their calving strategy and conservation status. While eastern migratory caribou move between the forest and tundra during spring and summer and are proposed to be Endangered, boreal caribou remain in the forest year-round and are listed as Threatened under the federal Species at Risk Act.</p> Results <p>Genome-wide analysis revealed that caribou are more genetically similar within provinces, regardless of whether they are eastern migratory or boreal. While boreal caribou showed a continuous genetic structure between Ontario and Quebec, eastern migratory caribou were genetically distinct between the two provinces. Although there is low genetic differentiation between ecotypes in both provinces, association analysis identified genomic variants that significantly distinguish them. These variants were different in each province and consisted of single nucleotide polymorphisms (SNPs) and small insertions-deletions (indels), with none located in regions exhibiting strong suppressed recombination, such as chromosomal inversions associated with “supergenes”. Instead, genomic variants were primarily found in non-coding regions or those linked to gene regulation. In Ontario, high levels of admixture were detected between ecotypes.</p> Conclusions <p>Our findings revealed that ecotypes in Ontario and Quebec are genetically distinguishable. The different polygenic variants found in each province and the absence of “supergenes” suggest a recent and independent evolution of the eastern migratory ecotype in each province. In Ontario, the levels of interbreeding between ecotypes indicate that the area of geographical overlap is larger than what the current distribution reflects. These results add to our current knowledge of caribou genetic structure and movement in the region and can provide insights for future management efforts.</p>