ITS sequence data in the present research has provided some useful insights resolving phylogenetic relationship among Eucalyptus species. It is to be complimented with rbcL, MatK and trnH-psbA gene study. There are 77 SNPs in an average in ITS fragment of 746 bps. Therefore, it contains highest percentage of variable characters in the gene. This study has shown a good distance between E. mitchelliana and the rest of species. The position of E. globulus and E. nitens is not clear. There is an overlap about E.dives and E.pauciflora. They are mixed up in E. stellulata, E. moorei and affin moorei are not separated by this gene. ITS, though more variable, it is found to be not so helpful for species identification in the Eucalyptus species.