The major histocompafibility complex （ MHC ） was used to study the genetic variation and differentiation in five populations （Yellow River population, Huai River population, Dongting Lake population, Poyang Lake population and Taihu Lake population） of Trionyx sinensis. The major results indicated that the polymorphism of the gene encoding MHC class Ⅰ molecule α2 domain in five populations of T. sinensis was rich. They were： （1） Some nucleotide sequences showed deletions or insertions. Seven different length sequences were obtained, of which 222 bp and 231 bp sequences were the major ones, existing in 42, 23 individuals respectively. （2） 41 different nucleotide sequences were got from 102 clones. The range of similarities of nucleotides was 0.386- 0.995, indicating relatively high difference. （3） Totally, there were 250 usable loci, of which 174 ones were polymorphic sites, accounting for 69.6 %. But there were some differences among populations as follows： ① The percentage of polymorphic loci was： Poyang Lake population（71.2 % ） 〉 Taihu Lake population（58.05 % ） 〉 Huai River population （57.69 % ） 〉 Yellow River population （55.32%） 〉 Dongting Lake population（48.09% ）. ② The range of nucleotide diversity index （π） was： Poyang Lake population （0.4273） 〉 Taihu Lake population（0.2872） 〉 Dongfing Lake population（0.2840） 〉 Yellow River population（0.2727） 〉 Huai River population（0.2463）. （4） The results of analysis of molecular variance （AMOVA） showed that there was significantly genetic differentiation between Taihu Lake population and Yellow River population, Huai River population, respectively, also between Huai River population and Dongting Lake population （ P 〈 0. 001 ）. （5） Yellow River and Huai River population, Dongting Lake and Taihu lake population clustered first respectively, then they clustered with Poyang Lake population by UPGMA and NJ method according to their nucleotide sequences average genetic distances, indicating an obvious divergence between Poyang Lake population and the other four populations on MHC.