Chinese alligator, Alligator sinensis, is a critically endangered endemic species under legislative protection in China. Result of recent investigations revealed that number of the alligators was continuously declining in the past 50 years and less than 150 individuals were surviving in the wild until 2000 years. In order to prevent the extinguishing of this species, two breeding farms were set up in early 1980s at Xuanzhou county, Anhui Province and Changxing County, Zhejiang Province respectively. After twenty years of breeding efforts, the number of captive individuals has been brought up to more than 9,000 in total, forming two separate captive subpopulations, Xuanzhou subpopulation (XZSP) and Changxing subpopulation (CXSP). Because of lack of the information regarding genetic diversity of the captive populations, 42 captive individuals including 33 individuals from XZSP and 9 from CXSP were sampled randomly to investigate their genetic status for the strategy in the next protection action. PCR method was adopted for amplification of mitochodrial DNA control region using primers designed in this research. After purification of PCR products, all of amplicons were sequenced directly with ABI BigDye Terminator Cycle Sequencing Ready Reaction Kit and ABI 310 genetic analyzer. Consequently, 5' end of control region with length of 462 base pair was obtained from 39 samples. Sequence alignment shows there is no any variation site in this range of control region among the individuals assayed here, namely only one haplotype of the region shared by these alligators. This result strongly indicates that the population of captive Chinese alligator is in very poor genetic diversity status. Reasons for the losing of genetic diversity in the population are mainly attributed to population depression and number of individual decreasing sharply in the past 50 years. Another factor accounting for the phenomena is the limit of founder number of captive population. Finally, authors proposed three pieces of advice for the genetic conservation of Chinese alligator.