Transposon is a DNA sequence with a certain length in the genome. DNA transposons are transposable elements which can move within their host genomes by changing their insertional positions in a process called transposition. The transposition can efficiently mediate by its transposase on “cut paste” approach. The strategy based on transposon insertional mutagenesis will be extremely powerful tool for trapping the target genes that control important trait in fish species. For a long time, the construction and application of DNA transposon system is blank in vertebrates. Recently, the powerful transposon tools has been developed for new area of research such as transgenesis and insertion mutagenesis in zebrafish, mice and other vertebrates, with the discovery of the active medaka Tol2, salmon SB, flounder Passport and goldfish Tgf2 and other cases of fish activity transposon. This article describes the latest progress of the fish DNA transposon, its structural characteristics and applications, and explores the feasibility of the transposon in mastering gene screening for important traits, functional explanation and genomics research in aquacultural fish species.