Population genetics is an important tool in marine resource management, but the collection of genetic data for marine mammals can be physically invasive and logistically challenging. Environmental DNA (eDNA) provides a non-invasive method for monitoring the presence of marine mammals. However, effective applications are limited by gaps in our knowledge about how eDNA behaves in the marine environment, and its use for population genetics is an emerging area. Here, we test the application of eDNA methods for the detection and characterization of intraspecific genetic diversity in Northwest Atlantic gray seals. Our objectives were to quantify gray seal eDNA concentration around haulout sites and to test the ability of eDNA sampling to detect mitochondrial control region haplotypes. Gray seal eDNA was consistently detected 50 meters from seal haulouts and could be detected up to 150 meters from shore. Up to 14 haplotypes were detected in a single water sample, and we observed a positive correlation between the frequency of haplotypes detected in our eDNA samples and the frequency of those haplotypes in the population, as determined by previous tissue sampling. This work demonstrates the ability of eDNA sampling to capture broad population genetic patterns from seals at haulout sites, with important considerations for future use in non-invasive monitoring and management.