RAPD was conducted to analyse the genetic variations of five populations in Trionyx sinensis ) Yellow River population, Huai River population, Dongting Lake populat ion, Poyang Lake population and Taihu Lake population, w ith 30 po lymorphic 10-based random primers selected from 97 ones. The major results indicated that the genetic diversity of the five populations in T . sinensis was rich. They were: ( 1) 341 bands were detected and 234 of them were polymorphic, accounted for 68. 6%. Two primers could amplify distinctive bands among the f ive populations. The appeared frequency of 1408bp band amplif ied by primer S105 was 20% in the Yellow River population, but it was 80%~ 90% in the other four populations. The range of appeared frequency of 438bp band amplified by primer S37 in the five populations was: Yellow River population 85% > Huai River population 65% > Dongting Lake population 55% > Poyang Lake population 40% > Taihu Lake population 20% , which indicated a genetic decline from Yellow River to Huai River, from middle reaches of Yangtze River to its lower reaches; ( 2) The range of proportion of polymorphic loci was: Taihu Lake population 59. 25% > Dongting Lake population 56. 52% > Poyang Lake population 55. 80% > Huai River population 55. 03% > Yellow River population 54. 43%, and there was no signif icant difference among the five populations( F= 0. 644< F0. 05; 4, 145 = 2. 45) . The genet ic diversity index ( P) was 0. 3644~ 0. 3833 in the populations; ( 3) The average genet ic similarity index within each population ranked as Huai River population 0. 782 > Yellow River population 0. 771 > Poyang Lake population 0. 768 > Dongting Lake population 0. 750 > Taihu Lake populat ion 0. 722. There was significant dif ference between Taihu Lake populat ion and Yellow River population,Huai River population and Poyang Lake populat ion( P < 0. 05) ; ( 4) The results of analysis of molecular variance( AMOVA) showed that there was signif icantly genetic breaking up between Yellow River population and Huai River population,Dongting Lake population, Poyang Lake population respectively, also between Taihu Lake population and Yellow River population, Huai River populat ion respectively ( P < 0. 001) ; ( 5) Yellow River and Huai River population, Dongting Lake and Poyang Lake population clustered f irst respectively, then they clustered with Taihu lake population by UPGMA and NJ method according to their genetic distances, which indicated that there was an obvious divergence between Taihu Lake population and the other four populations.