We used variation at microsatellite loci and in mitochondrial DNA (mtDNA) to detect and quantify (1) hybridization between the harbour porpoises Phocoena phocoena and the Dall’s porpoises Phoconoides dalli and (2) the genetic population structure of harbour porpoises in British Columbia (BC), Canada. We assayed variation across 262 individuals (204 putative harbour, 44 putative Dall’s, 9 putative hybrids, and 5 unidentified porpoises) obtained primarily from strandings and initially identified morphologically. Our assays identified 198 pure (probability ≥0.95) harbour porpoises, 37 pure Dall’s porpoises, and 27 individuals of mixed ancestry, and we found that hybrids between the 2 species occurred over a larger geographic range than previously known. Analysis of 8 microsatellite loci was used to estimate a value of FST between the Strait of Georgia region and waters outside this area that was low and non-significant (FST = 0.0025, p > 0.25). Cluster-based Bayesian analysis of population structure in harbour porpoises suggested a single genetic population across our sample area. Within the harbour porpoise, there were 50 mtDNA haplotypes that differed from each other by an average of 0.015 substitutions per nucleotide site. Hierarchical AMOVA indicated that there was no significant divergence between the waters within and the waters outside the Strait of Georgia region (ΦST = -0.022, p > 0.9). Our findings suggest that harbour porpoises inhabiting coastal waters of southern BC constitute a single genetic population, which should be reflected in management decisions. Our data also suggest that these management efforts should take into account occasional hybridization with sympatric Dall’s porpoise.