Abstract: Fifteen of Random Amplified Polymorphic DNAs (RAPD) primers with strong amplification of polymophic were selected from 50 of random primers. The selected 15 of primers were used to amplify genome DNAs of 22 of Puccinia obtegens samples and 3 of samples from Cephalanoplos setosum (Willd) Kitam, finally construct fingerprint pictures. The 25 samples consist of 9 urediospore samples collected from different locations, 6 samples with different spore types, 7 urediospore samples from same location collected at different dates and 3 samples from Cephalanoplos setosum (Willd) Kitam. The results showed that 204 mark bands were produced, 160 were polymorphic ones, polymorphism detection rate was 78.4%. The 3 groups of tested samples were divided into 3 cluster groups by SAS cluster analysis, respectively. The results proved that the tested samples had plenty of genetic polymorphisms, and further, their genetic relationship was related to origins, hosts, spore types and collecting times.