The genomic resources from human and several model organisms have been increased very fast since 1990. The techniques for developing genomic resources have already been very advanced and smart. These could make scientists see and improve organism in genomic level. For Chinese aquaculture scientists and aquatic industry , developing genomic resources and genetic tools for the native species are most important in the genomic era. The genomic resources and genetic tools for several aquatic species have been developed and some of them have been used in the marker based selection and other researches . The genome research work on aquaculture species was reviewed in this paper , especially a USDA genome project was focused. Some functional genomic research for aquatic animal was also discussed here. The importance and necessity of China aquaculture species genome project were discussed. Common carp and other cultured fishes in Cyprinidae such as grass carp , silver carp , bighead carp etc were recommended as the candidate species for genome research , because the output of all carps is almost up to 1/ 3 of total fisheries output in China. Common carp with another virtue for genome research is that there are much more families and strains in common carp than those in other cultured species in China , and those families and strains are the basis for genome research and mapping quantitative trait loci associated with important economic trait. Although the first linkage map of common carp made by Sun needs to be added with more markers for mapping QTL and Type Ⅰmarkers ,it has laid the groundwork for QTL mapping and marker2 assisted selection in common carp. Because the model organism zebrafish and common carp , grass carp and other carps cultured in China all belong to Cyprinidae , the China carp genome research will obtain a lot of useful information from zebrafish genome research. How the China carp genome program will be conducted and what kinds of strategy involved in this program were all suggested. How the results of the genome research of aquaculture species will be used in the aquaculture industry was reviewed and analyzed here.