Abstract:The genetic diversity of Sinocalycanthus chinensis populations in four different habitats, namely, scrub, evergreen broadleaved forest, Chinese fir forest and bamboo grove, was analyzed by polymorphic DNA technique. 12 primers were selected at random and 182 repeatable loci with 49 polymorphic loci were produced from 80 DNA samplings. The total average percentage of polymorphic loci was 26.92%. The percentage of polymorphic loci of four populations varied from 6.04% to 11.54% with an average of 8.93%, among which bamboo grove population was the highest and evergreen broadleaved forest population was the lowest with the order as follows: bamboo grove population＞scrub population＞Chinese fir population＞evergreen broadleaved forest population. The results of Shannon’s index and Nei’s index were in the same trend, the highest was scrub population, followed by bamboo grove population, and then was Chinese fir population, the lowest was evergreen broadleaved forest population. Analysis of molecular variance (AMOVA) demonstrated that the genetic differentiation among population was high. Variation among population occupied 71.91%, while that within population occupied only 28.09%. The gene differentiation coefficient among populations was 0.672 6. The gene flow among populations was very low, Nm=0.297 0. Cluster analysis showed Chinese fir population and scrub population got together first, then evergreen broadleaf forest population joined in, and the final population was the bamboo grove. It was obvious that different population had different genetic diversity, and there were remarkable genetic differentiation among populations.