This paper introduces the development of molecular marker-assisted breeding technology for aquatic species. Detecting markers linked to economic traits is the basis of molecular marker-assisted breeding. Therefore, this article focuses on the advances in genes or markers acquisition technology, explores the complexity of the relationship between genes or markers and traits, discusses the difficulty of accurately identifying genes or markers closely linked to economic traits, and points out that the difficulty is mainly due to the very complex influence of the genome on the formation of traits. In the past ten years, a number of varieties bred by molecular marker-assisted breeding technology have been applied in aquaculture, indicating that this new technology has played a positive role in promoting industrial technological progress. At the same time, the deficiencies of molecular marker-assisted breeding including genome-wide selection are caused by the extremely complicated and variable formation mechanism of fish trait, determining the characteristics of developmental stage theory.