Results of a past study on lean and siscowet lake trout (Salvelinus namaycush) reared under identical conditions from conception indicated that differences in growth and morphometry between these morphotypes have a genetic basis. Using these cultured lake trout, we found that siscowet lake trout had higher lipid levels and lower glycogen levels as compared with lean lake trout in skeletal muscle and liver. Lean lake trout also had higher circulating levels of lipids and glucose compared with siscowet lake trout. Analysis of F1 progeny from crosses of the cultured morphotypes showed that progeny of crosses between siscowet females and siscowet males had higher lipid levels than all other crosses. The combined results indicate that the lake trout morphotypes differ substantially in the storage of energy, which may be related to their specific life histories. Siscowets store energy preferentially as lipid and appear to be more efficient in moving lipid from the blood into the muscle and liver. The lipid in siscowets may be adaptive for regulating buoyancy as well as an essential energy reserve for reproduction.