Abstract:The genetic diversity of 41 sugarcane varieties bred in Guangdong Province was studied using 15 AFLP primer pairs. The results showed that the average polymorphic loci per primer pair were 61.5, and the percentage of polymorphism loci was 77.40%. The genetic similarity indexes of 41 varieties ranged from 0.5210 to 0.9211, with an average of 0.6842, which implied that the genetic diversity among the varieties was at middle level. The 41 varieties were clustered into two groups. Most of the varieties with close relationship in family-tree could be clustered into the same groups, such as YN81-762, YN85-1285 and YN86-295, as well as YT57-423, YT85-5 and YT85-177, but some varieties could not, such as YT83-251and YT83-271 which derived from the same cross “CP72-1210×Huanan 56-12”. The varieties selected at different periods showed remarkable differences in genetic diversity index (GDI). The varieties selected in 1980s were found to be the highest (GDI=0.3072), and the 1960s the lowest (GDI=0.1162). GDI of varieties from different Institutes revealed a little bit difference, but still kept in unremarkable level (from 0.2756 to 0.3061). The result indicated the genetic diversity would be increased by using new sources from sugarcane germplasm.