Selection efforts focused on adaptation to plant-based diets, particularly the ability to synthesize polyunsaturated fatty acids (PUFA), are now emerging in aquaculture. Landlocked salmon (Grand Lake population; GL) may differ from the commercial Saint John River (SJR) strain in terms of PUFA metabolism. The objective of this study was to determine if GL salmon can contribute toward broodstock selection for enhanced PUFA synthesis. Two diets containing either fish oil (FO) or plant-based oil (FO-free) were fed to the SJR and GL strains (∼58 g/fish) for 16 weeks. Growth, liver, and muscle fatty acid (FA) content, and transcript expression of lipid metabolism and inflammation-related genes were evaluated. GL salmon fed the FO diet showed reduced growth compared to SJR salmon (fed either diet); however, GL salmon fed the FO-free diet, growth was not significantly different compared to any group. In liver, SJR salmon fed the FO-free diet had higher levels of n-6 PUFAs (21.9%) compared to GL fed the same diet (15.9%); while GL salmon fed the FO-free diet had higher levels of monounsaturated FAs (48.9%) compared with SJR salmon fed the same diet (35.7%). 20:5n-3 and 22:6n-3 were the same in GL and SJR salmon liver and muscle, respectively, fed the FO-free diet. In liver, GL salmon fed the FO-free diet had higher acac and acly compared to all treatments and had higher fasb compared to both strains fed the FO-diet. GL salmon fed the FO-free diet had higher cd36c and fabp3b in liver compared to GL salmon fed the FO diet and SJR salmon fed either diet. GL salmon fed the FO-free diet had higher lect2a and pgds in liver compared to SJR salmon fed the FO-free diet. In muscle, GL salmon fed the FO-free diet had higher fadsd5 and fadsd6b compared with both strains fed the FO diet. These results suggest there is a genetic basis behind the potential for GL salmon to utilize FO-free diets more efficiently than SJR salmon, with regards to FA metabolism.