With the development of high-density and intensive aquaculture, the water environmental factors stress such as dissolved oxygen, water temperature and ammonia nitrogen has become the restricting factor. The harmful environmental conditions severely decrease the fish growth rate, reduce fish resistance and increase the susceptibility to diseases, which ultimately causes significant economic losses in aquaculture industry. The cultivation of new resistance fish varieties is one of the important solutions and attracting more attention which is becoming the research hot. In this review, we summarize the response mechanisms to environment stress including the temperature, hypoxia, ammonia nitrogen, nitrous nitrogen and saline-alkali stress from the physiology to molecules. Furthermore, the breeding progress of new fish varieties with environmental tolerance and the molecular markers (gene, SNP, SSR and so on) related to environmental tolerance traits are presented. Finally, we point out that the first national aquaculture germplasm resources investigation should be applied to explore excellent germplasm resources. The research on the integrated response mechanism of fish under multiple environmental factors stress should be strengthened. Meanwhile, the efficient and precise breeding technology of the new varieties of environment-tolerance fish should be established based on the modern molecular breeding technologies such as molecular marker-assisted breeding, genome selection breeding, gene editing breeding, molecular module design breeding and so on. This review will provide the reference for the new fish varieties breeding with resistance.