Understanding the impact of barriers and habitat fragmentation on the ecology and genetics of species is of broad interest to many biologists. In aquatic systems, hydroelectric dams often present an impenetrable barrier to migratory fish and can have negative effects on their persistence. Hydroelectric dams constructed in the Coquitlam and Alouette Rivers in the Fraser River drainage (British Columbia, Canada) in the early 1900s were thought to have led to complete loss of anadromous sockeye salmon from both rivers. For both reservoirs, recent water release programs resulted in the unexpected downstream migration of juvenile sockeye salmon and the subsequent upstream migration of adults towards the reservoir 2 years later. Here we investigate the evolutionary impact of dams on the sockeye salmon migration behavior by investigating the genetic distinction between migratory and non-migratory individuals within the Alouette and Coquitlam reservoirs. We also compare historical and contemporary genetic connectivity among 11 Lower Fraser River sockeye sites to infer recent population connectivity changes that might have been influenced by anthropogenic activities. Our molecular genetic analyses show a genetic distinction between the sea-run and resident individuals from the Coquitlam reservoir and population splitting time estimates suggest a very recent divergence between them. These results indicate a genetic component to migration behavior. For our broader survey from 11 sites, our comparisons suggest a general decline in gene flow, with a few interesting exceptions. In summary, our results suggest (i) early stage divergence between life history forms of sockeye salmon within one reservoir, and (ii) recent changes in genetic connectivity among Lower Fraser River populations; both of these results have potential recovery implications for historically migratory populations that were affected by anthropogenic barriers such as hydroelectric dams.