Surra, caused by Trypanosoma evansi, is an economically important disease of a wide range of domestic and wild animals. These parasites occur principally in blood and tissue fluids of their hosts as intercellular parasites causing a wide range of clinical manifestations. Since trypanosomes can effectively evade the host immune response by displaying an array of variable surface glycoproteins, attempts for developing a protective immunogen has not been met with success. PFR is one of the major constituent proteins of the flagella and structurally, it extends alongside of the axoneme from the flagellar pocket to the flagellum tip. This PFR is an elegant and stable lattice-like arrangement of protein filaments which is composed of two major and related proteins PFR1 and PFR2. PFR is vital for trypanosome motility and cell morphogenesis. Unlike the axoneme, which is broadly conserved among the eukaryotes, the PFR is restricted to kinetoplastids, euglenoids and dinoflagellates. So it has been considered as a vaccine target owing to its strategic location and invariable nature. In the present study, molecular cloning of PFR1 was carried out using pGEMÒ-T vector and the nucleotide sequence revealed 99.8% homology and only one nucleotide change at 867bp of PFR1 ORF between the Izatnagar and China isolates. The nucleotide sequence also showed 99.8%, 82.1%, 79.9%, 72.9% homology with Trypanosoma brucei, Trypanosoma cruzi, Leishmania infantum and Crithidia daenei, respectively. The deduced amino acid sequence of T. evansi PFR1 revealed 99.7% homology between Izatnagar and China isolate. It also showed 99.8%, 92.7%, 84.7%, 82.4% homology with T. brucei, T. cruzi, L. infantum and C. daenei, respectively.