The bioaccumulation of mercury (Hg) in fish is a potential threat to human health. Recent studies reported much lower methylmercury (MeHg) proportions but higher inorganic Hg (IHg) in farm-raised fish, however, the mechanism of Hg distribution in farm-raised fish body remains not well understood. In this study, we investigated the distributions of primary amino acids, MeHg and IHg in body tissues of two commonly farm-raised fish species (common carp: Cyprinus carpio; grass carp: Ctenopharyngodon idellus) in Guizhou Province, SW China, to understand the effects of amino acids on MeHg and IHg metabolism in farm-raised fish. The two fish species showed low THg concentrations (grass carp: 7.2 to 41.6 ng/g; common carp: 6.6 to 42.7 ng/g, dry weight) and low MeHg proportions (grass carp: 2-45%; common carp: 6- 37%) in their tissues, which are mainly due to the simple food web structures and the fast growth of the farm-raised fish. Positive correlations were observed between MeHg and several primary amino acids (e.g., cysteine, arginine, threonine, phenylalanine, leucine, valine, glutamate, cysteine, serine and tyrosine) in fish tissues, which may be driven by the formation of MeHg-Cys complexes within fish body. However, no clear correlations were observed between IHg and any primary amino acids, indicating the metabolic processes of IHg and MeHg are different. This study advances our understanding that cysteine and its related/derived amino acids may be an important driving force for MeHg distribution and translocation in fish.