In this study, we have bred a low-temperature-tolerant red tilapia TsR strain, but its growth and body size are not as good as the Nile species. To improve the low-temperature adaptability of Nile tilapia, we crossed TsR with n561A to establish F1, F2, and first backcross n561A for low-temperature resistance. These F2 crossed offspring were treated by cooling mode and collected survivors and victims respectively. then use Randomly Amplified Polymorphic DNA (RAPD) to genotype the genetic variation. To assess possible genetic mechanisms and low temperature of adaptation, we use 80 RAPD loci to fingerprint and clone the markers associated with the cold-tolerance. Then use the whole genome framework of Nile n561A strain to locate the marker selected Sequence Characterized Amplified Region (SCAR). Finally, we bred F2 which with low temperature resistant, cold-resistant associated gene marker and cloning, optimization, and positioning interlocked improve screening efficiency and shorten breeding.