Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers were used to detect the genetic diversity among 40 chewing cane germplasms. Polymorphism was identified by 23 RAPD primers and 28 ISSR primers in the germplasms. Two hundred and fifty bands were generated by RAPD with polymorphic bands accounting for 70% and similarity coefficient ranging from 0.68 to 1.00. And 301 bands were produced by ISSR with polymorphic bands accounting for 77.1% and similarity coefficient within 0.66 to 1.00. The germplasms were divided into 4 clusters by UPGMA: ClusterⅠcomposed of 32 individuals from Fujian，Jiangxi，Guizou，Yunnan，Guangxi, Cluster II containing cvs. Badila and Fengcengzipi, Cluster III covering hybrids (Baishan，Waigandan，Dudu，Wenling and artificial hybrid 474), Cluster Ⅳ only including cv. Huangpi. The significant correlation between RAPD and ISSR markers was observed (r=0.9746). ISSR was more suitable for the analysis of genetic diversity.