The internal transcribed spacer (ITS) was cloned with a primer pairs: 5'-GTC CCT GCC CTT TGT ACA-3' and 5'-CGC CGT TAC TAG GGG AAT CCT-3'. A total 821 bp were cloned including partial sequence of 18S ribosomal DNA flanking ITS region (5' end, 142 bp), full length ITS (587 bp), and partial sequence of 26S ribosomal DNA flanking ITS region (3' end, 92 bp). The ITS sequence of Saccharum officinarum is most closely related to S. spontaneum and S. robustum in the genus Sacharum, while most closely related to Erianthus spp. when it was compared across genus.