Abstract: Random amplified polymorphic DNA (RAPD) markers were used to measure the genetic diversity of Cercidiphyllum japonicum, an endangered plant in China.The experiment was implemented among 11 natural populations from Zhejiang, Anhui, Hunan, Hubei, Sichuan, Shannxi and Henan of C. japonicum. A total of 691 DNA fragments were amplified from 20 RAPD primers, of which 328 were polymorphic, account for 47.5 % of all bands. AMOVA was used to determine the variation within and among populations. Results indicated that the variation among populations was 0.479 7 and that within populations was 52.03%. The gene flow was 0.542 4 based on the Nei gene differentiation index indicated that the gene intercourse was difficult among populations. Results of UPGMA cluster analysis indicated that the genetic distance between the population of Shexian Anhui and Jiyuan Henan was the largest among populations. Genetic drift might have enhanced genetic differentiation within populations. In order to protect the species, preserving the habitat and breeding the seedlings to expand the species were suggested.