Membrane fatty acid desaturase (FADS)‐like superfamily proteins (FADSs) are essential for the synthesis of unsaturated fatty acids (UFAs). Recently, studies on FADS in fishes have mostly focused on marine species, and a comprehensive analysis of the FADS superfamily, including the FADS, stearoyl‐CoA desaturase (SCD), and sphingolipid delta 4‐desaturase (DEGS) families, in freshwater economic fishes is urgently required. To this end, we conducted a thorough analysis of the number, gene/protein structure, chromosomal location, gene linkage map, phylogeny, and expression of the FADS superfamily. We identified 156FADSsgenes in the genome of 27 representative species. Notably,FADS1andSCD5were lost in most freshwater fish and other teleosts. All FADSs proteins contain 4 transmembrane helices and 2–3 amphipathic α‐helices.FADSsin the same family are often linked on the same chromosome; moreover,FADSandSCDorDEGSare frequently collocated on the same chromosome. In addition, FADS, SCD, and DEGS family proteins share similar evolutionary patterns. Interestingly,FADS6, as a member of theFADSfamily, exhibits a similar gene structure and chromosome location to that ofSCDfamily members, which may be the transitional form ofFADSandSCD. This study shed light on the type, structure, and phylogenetic relationship of FADSs in freshwater fishes, offering a new perspective into the functional mechanism analysis of FADSs.