The genetic diversity of Trollius populations from different origins were analyzed by RAPD marker in molecular level, and which will be helpful for population evaluation and for further reasonable protection of Trollius germplasm resources in China. 194 score able bands were amplified in total with 108 bands having polymorphism amplified with 30 RAPD primers in the genome DNA of 24 Trollius populations, and the percentage of polymorphic loci was 55.67%. The general gene diversity index was 0.1460, and the genetic diversity index within populations was 0.0591, the Shannon’s information index of all was 0.2248; Based on the UPGMA cluster analysis method, 24 Trollius populations were classified into three main groups, and the coefficient of genetic differentiation was 0.6902, mean gene flow value was 0.2244 based on the general genetic diversity and genetic diversity within populations. The analysis results showed that the genetic diversity of Trollius populations in China were not abundant, and protection strategies should be carried out on Trollius populations with significant genetic diversity.