Dams have negatively affected freshwater biodiversity throughout the world. These negative effects tend to be exacerbated for aquatic taxa with migratory life histories, and for taxa whose habitat is fundamentally altered by the formation of large reservoirs. Sauger (Sander candadensis; Percidae), large-bodied migratory fishes native to North America, have seen population declines over much of the species' range, and dams are often implicated for their role in blocking access to spawning habitat and otherwise negatively affecting river habitat. Furthermore, hybridization appears to be more frequent between sauger and walleye in the reservoirs formed by large dams. In this study, we examine the role of dams in altering sauger population connectivity and facilitating hybridization with introduced walleye in Wyoming's Wind River and Bighorn River systems. We collected genomic data from individuals sampled over a large spatial scale and replicated sampling throughout the spawning season, with the intent to capture potential variation in hybridization prevalence or genomic divergence between sauger with different life histories. The timing of sampling was not related to hybridization prevalence or population divergence, suggesting limited genetic differences between sauger spawning in different time and places. Overall, there was limited hybridization detected, however, hybridization was most prevalent in Boysen Reservoir (a large impounded section of the Wind River). Dams in the lower Wind River and upper Bighorn River were associated with population divergence between sauger upstream and downstream of the dams, and demographic models suggest that this divergence has occurred in concordance with the construction of the dam. Sauger upstream of the dams exhibited substantially lower estimates of genetic diversity, which implies that disrupted connectivity between Wind River and Bighorn River sauger populations may already be causing negative demographic effects. This research points towards the importance of considering the evolutionary consequences of dams on fish populations in addition to the threats they pose to population persistence.