Genetic diversity of 13 cannabis populations from different sources was analyzed by POPGENE 3.2 Software. AFLP analysis showed that the Yunnan population had the highest level of genetic diversity (PPB = 88.82%，h = 0.3011，I = 0.4571)，and then the Heilongjiang population (PPB = 75.66%，h = 0.2572，I = 0.3897). The percentage of polymorphic loci (PPB) of 13 Cannabis populations was 92.11%. Nei's total genetic diversity (Ht) was 0.3837，the genetic diversity (Hs) was 0.1640. Coefficient of genetic differentiation among populations (Gst) was 0.5725，it means that 57.25% of the total genetic variation occurred among populations，and 42.75% genetic variation in different populations. To further analyze the genetic differentiation among populations, the genetic distance and genetic identity of Cannabis were calculated according to Nei's (1978) method. The results showed that the genetic identity among populations was from 0.6556 to 0.9258，the highest degree of consensus between Guangxi population and Sichuan population was 0.9258. Genetic identity between Yunnan population and Guizhou population or Sichuan population were 0.9196 and 0.9173. Gansu and Shanxi population with lowest genetic identity in all populations was 0.6556. The results indicated that rich genetic diversity among 13 cannabis populations. This study analyzed genetic diversity of cannabis populations in molecular level，provided scientific evidence for the protection of seeds, breeding, evolution study of industrial hemp.