ISSR marker was used to identify the genetic diversity and relationship of 36 common bean cultivars collected from the scientific research institutes in Jilin Province. 20 primers were screened out from the 100 ISSR primers. The genetic similarity coefficients were calculated with NTSYSpc2.10 and the cluster analysis was conducted by UPGMA. The results showed that 87 DNA fragments were amplified by PCR, among which 76 ones were polymorphic and the polymorphism frequency was 87.36%. The results showed that there was relatively high genetic diversity among the accessions. The values of genetic similarity coefficients among the accessions were between 0.65 and 0.89. The 36 common bean accessions were divided into four groups by UPGMA, the cluster analysis conducted with UPGMA showed that the clustering results were closely correlated with the source of common bean and the genetic distance between cultivar No.20 and other cultivars was relatively remote. The specific makers of cultivar No.20 based on primer 840 amplified an extra band in 1100bp, the specific makers of cultivar No.27 based on primer 861 amplified an absent band in 1000bp, and the specific makers of cultivar No.30 based on primer 846 amplified an absent band in 1050bp. 3 specific makers could quickly identify cultivar no.20, No.27 and No.31 from all the 36 common bean varieties.