To well evaluate and utilize sugarcane germplasm,we analyzed the genetic diversity and fingerprint of 45 elite sugarcane germplasms,including 29 clones of germplasm innovation in Yunnan and 16 major parents,by simple sequence repeat (SSR) markers with 6 pairs of primers.The results showed that 6 primer pairs produced 104 bands,in which 101 were polymorphic,the percentage of polymorphic bands was 97.25%;the genetic similarity coefficient (GS) ranged from 0.235 3 to 0.891 3 with an average of 0.563 3 in 45 germplasms,and the genetic similarity coefficient ranged from 0.301 6 to 0.755 6 in 16 major parents of sugarcane,the number of specific bands in Yunnan germplasms of sugarcane innovation were 14-folds more than those in the major parents,containing Saccharum spontaneum,Saccharum robustum,Erianthus arundinaceum and Erianthus rockii.According to the similarity coefficient scope between 16 major parents of sugarcane,the 45 germplasms were clustered into 6 groups at 0.43,their genetic relationships were more far relatively,and suitable to be hybrid between the germplams.The rate of distinguishing cultivars by cluster UPGMA (RDVC%) was analyzed for each pair of primers,the value of polymorphism information content (PIC) ranged from 0.975 8 to 0.976 9,the standard fingerprint of Yunnan germplasms of sugarcane innovation was established by the primers of MSSCIR21 and SMC1047HA which had the highest efficiency primer combinations in identifying these sugarcane germplasms,and distinguish all the species in the similarity coefficient was 0.85,the identification accuracy is 100%,each germplasm has an unique fingerprint,and 16 major parents and 29 germplasm innovation can be distinguish,thus can be used in the hybridization,identification and intellectual property protection.