The partial mitochondrial DNA D-Loop sequence was amplified in two populations(Egyptian and 88 strain) of Nile tilapia(Oreochromis niloticus)(AJ and XH) and Blue tilapia(‘Xia′ao No.1',O.aureus)(ALY) by PCR technique.The length of this region was 575-581 bp.Compared with its homology,one conserved block(CSB-D) in the central conserved sequence block domain(CSB) and three conserved sequence blocks(CSB1,CSB2,CSB3) in the conserved sequence block domain(CSB) were successfullyidentified.A total of 28 haplotypes were detected in 76 individualities.The number of haplotypes was 12 in the AJ population,10 in the XH population and 9 in the ALY population.Only one haplotype(XH06) was shared by three populations,and one haplotype(XH10) was shared by AJ and XH populations.Genetic diversity analysis indicated some genetic differentiations between AJ and XH(N_m=0.77),AJ and ALY(N_m=0.02),as well as XH and ALY(N_m=0.02).The nucleotide diversity(Psub>i) of AJ(0.042 4) or XH(0.031 1) was higher than that of ALY(0.001 2).It could be concluded that the purity of ALY was much higher,and that AJ and XH had a high level genetic diversity.The mtDNA D-Loop region could reflect the genetic resource characteristics and could be used to study genetic diversity of tilapia populations.