Comparative analyses of the roar vocalization of male harbor seals from ten sites throughout their distribution showed that vocal variation occurs at the oceanic, regional, population, and subpopulation level. Genetic barriers based on the physical distance between harbor seal populations present a likely explanation for some of the observed vocal variation. However, site-specific vocal variations were present between genetically mixed subpopulations in California. A tree-based classification analysis grouped Scottish populations together with eastern Pacific sites, rather than amongst Atlantic sites as would be expected if variation was based purely on genetics. Lastly, within the classification tree no individual vocal parameter was consistently responsible for consecutive splits between geographic sites. Combined, these factors suggest that site-specific variation influences the development of vocal structure in harbor seals and these factors may provide evidence for the occurrence of vocal dialects.