The evolution of population structure in marine organisms and its relevance to conservation has recently received increasing attention. We tested the degree of genetic subdivision among ten populations of copper rockfish (Sebastes caurinus) representing paired samples of outer coast and the heads of five replicate sounds on the west coast of Vancouver Island, British Columbia using 17 microsatellite DNA loci. Overall, subdivision (FST) was low (FST = 0.031), but consistently higher between paired coast and head of inlet sites (mean FST = 0.047) compared to among five coast sites (mean FST = -0.001) or among the five head of inlet sites (mean FST = 0.026). Heterozygosity, allelic richness, and estimates of effective population size were also consistently lower in head of inlet sites than in coast sites. Bayesian analysis of population structure identified two genetic groups across all samples, a single genetic group amongst only coast samples, two genetic groups amongst head of inlet samples, and two genetic groups within each sound analysed separately. Head of inlet copper rockfish were also consistently shorter with lower condition factors, and grew more slowly than fish collected from coast sites. Our results implicate coast- head of inlet habitat transitions in driving the evolution of population structure, likely resulting from reduced physical connectivity and selection against immigrants in contrasting environments. Coast sites appear to be well served by existing marine protected areas. By contrast, head of inlet sites may require more specific local conservation measures as they appear to be less well connected to adjacent coast sites as well as to each other.