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The effects of low salinity on fatty acid and free amino acid (FAA) composition in muscles of swimming crab, Portunus trituberculatus, were investigated in this study. The swimming crabs were reared for 5 weeks under two different experimental treatments (the 12 ppt group and the 24 ppt group). Then, composition of fatty acids and free amino acids in total muscles was measured using gas chromatography–mass spectrometry (GC‐MS) with external standard method and liquid chromatography–mass spectrometer (LC‐MS) with internal standard method respectively. Results of fatty acid analysis showed that C18:1n9c, C20:5n3 (EPA) and C22:6n3 (DHA) were the dominating fatty acids in muscle tissues of P. trituberculatus. There was an extremely significant increase in contents of total fatty acids (TFA), total saturated fatty acids (SFA), total monounsaturated fatty acid (MUFA) and total polyunsaturated fatty acid (PUFA) in muscle tissues of P. trituberculatus with low salinity treatment (12 ppt) compared with those cultured in seawater (24 ppt) (p < 0.01). Results of free amino acid analysis showed that the content of total free amino acids (TFAA) significantly decreased in muscle tissues of P. trituberculatus with low salinity treatment compared with those in seawater (p < 0.05). Among all flavour‐tasting FAAs, the umami FAA content was extremely significantly higher in low salinity group compared with control group (p < 0.01); the sweetish FAA content was significantly lower in low salinity group while the bitter taste of FAA content had no significant differences between two groups. [ABSTRACT FROM AUTHOR]