The present research was aimed at a comparative analysis of free amino acid (FAA) levels in the muscle tissue of herbivorous and predatory fish. The FAA concentration in the muscle tissue samples from bighead carp and wels catfish was determined by ion-exchange chromatography. The bighead carp muscle tissue, as compared to that of wels catfish, showed significantly higher concentrations of arginine, histidine, methionine, phenyloalanine, alanine, asparagine, serine, glycine, and taurine, but significantly lower levels of isoleucine, leucine, threonine, valine, glutamine, cystationine, β-alanine, ethanoloamine, as well as aspartic, glutamic, cysteic, α- and γ-aminobutyric acids. The muscle tissues of bighead carp and wels catfish did not differ significantly in the levels of cystine, lysine, tryptophan, tyrosine, α-aminoadipic acid, cytrulline, ornithine and 1-methyl-histidine. Proline was detected only in the wels catfish muscle. The results obtained have shown differences in free amino acid concentration in muscle tissue of examined fish. A differentiated natural diet induces changes in free amino acid content in fish tissues. Knowledge of levels of free amino acids which are precursors for biogenic amines facilitates setting the safety criteria for fish and fishery products from species other than those mentioned in the Commission Regulation No 2073/2005