Genomics focuses on dissection of genome structure and function to provide a molecular basis for understanding the genetic background. In a pivotal step,the expense of whole genome sequencing has been largely eliminated by the rapid updating of sequencing technology,leading to increasing numbers of decoded genomes of aquatic organisms, driving the aquaculture industry into the genomic era. Multiple aquatic areas have been influenced by these findings, such as accelerated generation shift in the seed industry and the process of breeding improved lines. In this article, we have summarized the latest domestic and international progress of aquatic animals in nine aspects, including WGS and fine mapping,construction of high density genetic/physical maps, traitrelated marker/genes screening, as well as sex control,genome editing, and other molecular breeding technologies. Finally, the existing problems in this field have been discussed and five future counter measures have been proposed accordingly. Genomics focuses on dissection of genome structure and function to provide a molecular basis for understanding the genetic background. In a pivotal step, the expense of whole genome sequencing has been eliminated eliminated by the rapid updating of sequencing technology, leading to increasing numbers of decoded genomes of aquatic organisms, driving the aquaculture industry into the genomic era. driving through the aquaculture industry into the genomic era. and international progress of aquatic animals in nine aspects, including WGS and fine mapping, construction of high density genetic / physical maps, traitrelated marker / genes screening, as well as sex control, genome editing, and other molecular breeding technologies. problems in this field have been discussed and five future countermeasures have been proposed acco rdingly.