Abstract: [Objective and Method]The genetic diversity of 29 Carthamus tinctorius L.cultivated varieties in Xinjiang were tested with RAPD and ISSR techniques.[Result]156 and 112 DNA bands were amplified with 20 RAPD and 18 ISSR primers respectively,and the percentage of polymorphic bands (PPB) was 92.31; and 93.77; respectively. Effective number of alleles Ne,Nei's index H ,the Shannon information index were 1.508 1 and 1.513 7,0.311 5 and 0.341 6,0.473 8 and 0.479 8 respectively.The UPGMA clustering indicated that the genetic distance of RAPD and ISSR were 0.108 2～2.054 1 and 0.123 4～2.153 5 .[Conclusion]These above results showed that there was relatively rich genetic variations in safflower. Comparison between the two marker systems showed that ISSR was better than RAPD in terms of reproducibility and ability of detecting genetic polymorphism.Mantel test revealed that the analyzed result of the two marker had significant correlation r=0.963.