Dietary reliance of brown trout on low-quality terrestrial prey, deprived of n-3 LC-PUFA, increased in sympatry with invasive brook trout. Higher reliance on terrestrial prey of sympatric brown trout resulted in lower content of EPA in their muscle tissues compare to the allopatric conspecifics. In the sympatric populations, the content of the short-chain ALA increased and the content of the long-chain DHA decreased in muscle tissues with increasing reliance on the low-quality terrestrial prey, but the relative content of ALA and DHA in allopatric brown trout was not related to the diet quality. Sex had no effect on diet quality and muscle content of n-3 LC-PUFA, but larger (and presumably older, i.e., Bowker 1995; Öhlund et al. 2008) individuals relied more on terrestrial prey and consequently had lower relative content of n-3 LC-PUFA in muscles. We found that the relative content of DHA in muscle tissues was positively related to the encephalization of brown trout (i.e., higher relative brain size after controlling for the body size). These findings demonstrate that intra-specific differences in diet quality in wild vertebrates, foraging at interface of aquatic and terrestrial food webs, are linked to their brain size. In addition, our findings indicate that external stressors, such as competition with an invasive species, can reduce the capacity of consumers to synthetize and retain DHA for brain development.