The mtDNA control region of GIFT strain Oreochromis niloticus in F₀, F_6-9 generation were amplified and sequenced. 225 loci were polymorphic and accounted for 24.94% in 902 base pairs of 47 samples. The ratio of polymorphic loci was highest in F₀, and decreased with selection proccessing. Nucleotide diversity index were 0.074 02, 0.068 72, 0.064 15, 0.049 52, 0.044 55 for F₀, F₆, F₇, F₈, F₉, respectively. The ratio of polymorphic loci, nucleotide diversity index among these five generations showed that the selected populations were getting purer after selection procession. Genetic distances between F₀ and these four selected populations were increased with selection procession, which suggested that selection could result in genetic differentiation just as caused by longterm geographical isolation.