OBJECTIVE： To study the phylogenetic relationships of 3 basic plants of Tibetan medicine “Dida”， such as Swertia puricea， Wertia mileensis， Halenia elliptica. METHODS： ISSR technology was used for PCR amplification of 9 samples of S. puricea （ZT-1 to ZT-5 from Gantongsi in Dali Cangshan， ZC-1 to ZC-4 from Binchuan county of Dali）， 2 samples of W. mileensis （QYD-1 to QYD-2） and 2 samples of H. elliptica （HM-1 to HM-2）. Using DNA genome of S. puricea as template， 8 primers were screened and used for PCR reaction. The PCR amplification products were read by hand， the original data matrix was established， and the polymorphic band ratio was calculated. At the same time， genetic similarity coefficient was calculated by using NTSYS 2.1 software， and UPGMA method was used to draw cluster diagram. RESULTS： A total of 113 clear and identifiable amplification product bands were obtained by 8 ISSR primers. The rate of polymorphic site was 100％. The genetic similarity coefficients for totally 13 samples of S. puricea， W. mileensis and H. elliptica ranged 0.301-0.500. Intraspecific genetic similarity coefficients for 9 samples of S. puricea ranged from 0.752 to 0.929. The cluster analysis showed， when the range line was 0.410， 13 samples could be divided into three groups， i.e. S. puricea， W. mileensis， H. elliptica； when the range line was 0.780， 9 samples of S. purpurea could be divided into 2 subgroups， one of which was only sample ZT-1 collected from Gantongsi in Cangshan， and the other contained the remaining 8 samples. CONCLUSIONS： ISSR technology can be used to identify S. punicea， S. glabra and H. elliptica at the molecular level. S. punicea has some genetic relationship with S. glabra and H. elliptica， but the genetic relationship is relatively distant and the genetic difference is large. S. punicea from two different locations in Dali area has little genetic difference and close relationship， but it shows abundant genetic diversity.