Abstract: To evaluate the effect of the present breeding ways on genetic structure and breeding potential of Egyptian strain of Oreochromis niloticus, we analyzed the variation of mitochondrial DNA D-loop region in their three generations (80 individuals). The results show that: 1) The length of the region sequences was 552~555 bp; 52 variable sites and 12 haplotypes were detected. The average haplotype diversity was 0.569. 2) The nucleotide polymorphisms (P_i) of three generations were 0.021 9, 0.040 3 and 0.039 7, respectively, each generation showing high polymorphism in the mitochondrial genetic diversity. 3) F₁ generation contained five haplotypes; F₂ generation contained seven haplotypes; F₃ generation contained seven haplotypes. The three generations shared two haplotupes, and F₁ and F₂ generations shared a haplotype. The haplotypes of three generations crossed each other in the NJ tree and no unique clade of haplotype existed in each generation. It is concluded that there was no significant variation in genetic structure at the control region sequence in the three generations. The genetic information among three generations of O.niloticus was stable by the present breeding ways.