Abstract: ObjectiveInfluences of artificial selection preference on Oreochromis aureus genetic diversity were studied to provide some reference for O. aureus breeding and production. MethodSequence and phylogeny of mitochondrion DNA D-loop region, Cytb gene and COI gene from 140 individuals of two O. aureus populations(70 from Nama population and 70 from Wuming population) were studied. Meanwhile, 20 pairs of microsatellite primers were applied to analyze the genetic diversity. ResultThirty haplotypes were detected based on D-loop region and six of them were shared haplotypes; twen-ty-three were detected based on CoI gene and sixteen were shared haplotypes; fourteen were detected based on Cytb gene and ten were shared haplotypes. Phylogenetic trees based on D-loop region sequence, CoI gene and Cytb gene indicated that the individuals from Wuming population and Nama population interveined and showed no obvious geographical difference . Evolution topology of phylogenetic trees based on Neighbor-joining ( NJ ) method and Minimum-evolution (ME)method were similar. All 20 pairs of microsatellite primers could obtain stable and effective amplified bands from O. aureus, and 18 microsatellite loci presented polymorphism . Average allele numbers (Ne) for Nama population and Wuming population were 6.5000 and 7.9444 respectively, average effective allele numbers(Ne) were 3.9857 and 4.7268, average observed heterozygosity (Ho) were 0.7123 and 0.7752, average expected heterozygosity (He) were 0.9614 and 0.9711, average Nei expected heterozygosity were 0.7017 and 0.7636. All the indexes for Wuming population were higher than those of Nama population. There was obvious difference of coefficient of genetic differentiation (Fst) at different mi-crosatellite loci, ranging from 0.0173(GM241)-0.2318(UNH868) with an average of 0.0997. From the perspective of inbreeding coefficient of single group(Fis) and inbreeding coefficient of total groups(Fit), the values of all microsatellite loci were negative. ConclusionGenetic diversity of Wuming population which was artificially selected for short term is more abundant than that of Nama population which was artificially selected for long time. In another words , influence of artificial selection on mitochondria DNA is small in short term.