Chinese alligator (Alligator sinensis) is an endemic species in China. The likely extinction of it in the wild has been recognised. To prevent this species becoming extinct, the Anhui Research Centre of Chinese Alligator Reproduction (ARCCAR) was established in Xuanzhou, Anhui Province in 1979, where has been established the largest captive population of Chinese alligator (XZSP) in the world. Another farm (CXSP) was established by villagers in Changxin, Zhejiang Province. The results of an investigation of the two captive subpopulation structures by genetic analysis are presented in this paper. We examined the genetic variation in the two captive subpopulations using RAPDs. Thirty-one random primers were selected among 199 random primers screened. A total of 193 reproducible RAPD fragments were scored among 43 individuals, of which 21 (10.88%) were polymorphic. The genetic distances between 43 individuals ranged from 0 to 0.0376 with average of 0.0104 0.0055 S. E. The genetic similarity in CXSP (0.9948 0.0029 S. E.) was higher than that in XZSP (0.9894 0.0055 S.E.). The founder effect is a possible explanation for very low genetic variation in CXSP. Analysis of the RAPD data showed that the mean phenotypic band frequencies of each polymorphic loci was 0.6656 0.3730 S. E. The lowest phenotypic band frequency (0.0233) was found in four of those polymorphic loci. There was no genetic difference between the two subpopulations (Dij=0.0009). According to the dendrogram and the distribution of polymorphic fragments in two subpopulations, CXSP originated genetically from XZSP. This paper summarises a preliminary research on genetic structure in populations of Chinese alligator. Although there is higher genetic similary (0.9896 0.0055 S. E.) in captive population of A. sinensis, we did not determine whether or not loss of genetic variation had occurred in relation to a wild control population. The data of malformed offspring will be collected carefully, and wild samples be added to set up a control population in future study.