This study quantified stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotopes, polychlorinated biphenyl (PCB) concentrations and growth rates among multiple genetic strains of Lake Ontario lake trout (Salvelinus namaycush) to evaluate the potential role of genetics in these parameters. Fish ranging in age from 1 to 31 years (n = 72) and representing nine genetic strains including wild-recruits to hatchery fish derived from Lakes Ontario, Superior and Champlain watersheds, and individuals of unknown hatchery origin. Carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotope values averaged −22.2 ‰ and 17.4 ‰, respectively, but did not differ significantly among genetic strains. ΣPCB concentrations ranged from 42 to 1820 ng/g and varied significantly among individuals including those of similar age and genetic strain. For example, Sum PCB (ΣPCB) concentrations among 7-year-old fish (n = 16) ranged from 159 to 607 ng/g, which compares to growth rates of 3.5 – 32.9 %/yr for these same fish. Multivariate analysis of stable isotope and PCB profiles, however, provided considerable resolution among the strains. For example, fish of unknown hatchery origin ordinated most similar to Seneca Lake fish, the predominant strain stocked in Lake Ontario. Wild fish had a unique ordination with only Lake Superior Klondike strain fish overlapping into their ordination space. Lakes Champlain and Superior strain individuals had similar ordinations but did not overlap substantially with wild or Klondike strain fish. Combined, these differences agree with the ecologies described for these strains in their native ecosystems suggesting that insight can be gained from strain specific evaluations of ecological tracers and these pollutants among Great Lakes lake trout.