In this paper, the development and application of related technologies in aquatic genome research are reviewed. Taking the appearance of the next-generation sequencing (NGS) technology as a demarcation point, we firstly looked back to the researches of genetics and molecular biology of aquatic organisms in the early stages, and the basic researches for the whole-genome sequencing. And then we emphatically introduced the development of the NGS technology application for whole-genome sequencing and economic traits analysis. At last, the development trend of aquatic organisms whole-genome researches is prospected. The genetic mechanism of economic traits of aquatic organisms is highly complex, thus there are still a lot of difficulties in explaining the genetic mechanism at the whole-genome level. However, it is a basic law that trait is determined by genes, so the exploration will still be fascinating.