The amount and extent of dispersal can have a large effect on the evolutionary trajectory, dynamics and structure of populations. Thus, understanding patterns of genetic structure provide information about the needs and approaches for population management and species conservation. To date studies addressing the population structure of Canada lynx (Lynx canadensis) have been surprisingly equivocal, despite a large amount of research quantifying population cyclicity and synchrony and the species' species at-risk status in the contiguous United States and eastern provinces of Canada. Here we use 17 microsatellite loci to conduct a large-scale genetic structuring assessment for Canada lynx, including most of its geographic range from Alaska to Newfoundland. We found large differentiation between lynx populations on the island of Newfoundland and those on the mainland. Yet, contrary to previous studies we found little genetic differentiation (F ST , D est , R ST ) owing to the Rocky Mountains, but some evidence of a subtle gene flow restriction between Ontario and Manitoba as previously proposed to be the result of a climatic barrier. Bayesian clustering analysis, however, only suggested two genetic clusters, one consisting of lynx from Newfoundland, and the other consisting of lynx from the rest of the North American range. Because Canada lynx are harvested for fur across most of their range, our results are informative for effective management strategies (e.g., defining management units) aimed at ensuring long-term population connectivity and species persistence.