The DNA of kinetoplastid like Leishmania and Trypanosoma, thymine (T) base is modified into Dglucosyl- hydroxy-methyluracil (base J). The J-binding protein (JBP) plays a crucial role in conversion of base T into base J. In this study, comparison of JBP is done at both : the sequence and structural level in both the species in order to examine the possibility of a common drug target. Several tools and bio-informatics approaches have been used for the three-dimensional structural modeling, validation of modeled structures, sequence and structural alignment, R-R contact propensity and docking of JBP with modeled DNA. The protein sequences are modeled by the ModWeb server by using 2XSE as a template. More than 95% residues are fallen into allowed region of modeled structures of JBP of both the species. So these structures are used in the further analysis. The sequence of JBP of L.major and T.bucei are not identical but it these are much similar at the structural level. The L.major is much similar with template than the T.brucei. In the conservation profile. Residue-residue contact propensity is higher in L.major than T.brucei. The JBP of both the species shows more or less similar pattern of interaction with the thymine base present in the telomeric sequences. Subsequently these thymine bases are modified during the binding process. The interaction may be check by performed mutation on the thymine. On the basis of structural similarity and interaction with DNA, it might be used as a common drug target for drug design in both the species.