This project utilized genetic techniques to determine the spatial scale at which populations of Pacific Harbor Seals (Phoca vitulina richardsi) are functionally isolated. Using a suite of both nuclear and mitochondrial DNA markers, the differentiation among harbor seals sampled from Vancouver Island south to Florence, Oregon was analyzed. Thirty unique mtDNA haplotypes were identified, and a minimum spanning network shows that haplotype lineages are not geographically isolated. However, among-group AMOVA analyses indicate regional differentiation in haplotype frequencies (FST = 0.069, p < 0.0012). Analysis of eight microsatellite loci suggests subtler divergence between Puget Sound and coastal animals and no differentiation among coastal regions. The disparity between results from these two marker types suggests males are contributing more to genetic exchange among areas than females and may be important vectors of gene flow for harbor seals in this region. In general, these patterns support current stock boundaries but indicate less genetic divergence among coastal areas than behavioral observations and spatial scales of differentiation reported for this subspecies in other regions would predict.