On the analysis of genetic difference of different local lines of edible sugarcane, the internal transcribed spacer (ITS) of ribosome DNA (rDNA) was cloned and cleavage with restriction endonucleases. Among the 16 lines tested, total 89 bands were obtained and in which 13 bands are unique to Guan-Shan (5) and Chi-Sang (8). With HpaII, local lines of Guan-Shan and Chi-Sang could be distinguished from the lines cultivated in western Taiwan, indicating that there are considerable differences exist between eastern and western populations. The polymorphic band patterns indicate that there are some differences among lines cultivated in different districts.