Abstract: The genetic structure of 11 different populations of floral-color Anemone obtusiloba in 4 different areas of Gannan were evaluated using random amplified polymorphism DNA ( RAPD) .The results showed that the genetic diversity in Anemone obtusiloba populations was quite high: The Shannon index ( I) was 0.6025 and Nei's gene diversity ( H) was 0.4166. Moreover, the differentiation level among populations was low based on Nei's Gst value and analysis of molecular variance ( AMOVA) .Less than 33% of genetic diversity was attributed to the differentiation among populations while more than 67% resided within the different populations.According to unweighted pair group method using arithmetic averages ( UPGMA) result, 11 populations of A.obtusiloba were clustered into 3 groups. Further correlation analysis showed that genetic diversity and distance correlated with geographical distribution and soil nutrition.