Abstract: In this study we performed the sequence and phylogenetic analysis of peste des petits ruminants (PPR) virus isolates recovered from natural disease outbreaks in goats of central India. A total of 58 clinical samples comprised of blood, nasal/oral/rectal swabs were collected from 3 natural PPR disease outbreaks. The samples were tested by using N protein based MAb based sandwich ELISA (sELISA) and subsequently RT-PCR targeting Fusion (F) and Nucleoprotein (N) genes of PPR virus. The F and N gene specific PCR amplicons were sequenced and assessed for sequence variations with existing and circulating PPR virus strains and vaccine isolates. The results of this study presents PPR virus antigen in 48.27% clinical samples (28/58) using sELISA confirming this outbreak of PPR in goats. Amplification with primers F1/F2 for F gene yielded an expected amplicon of 372 bp and N1/N2 primer sets yielded an amplicon of 463 bp for N gene in reference vaccine virus as well as 28 field samples. In phylogeny, different patterns of branching based on N and F gene sequences and clustering of many of the central Indian PPR virus isolates with isolates from bordering countries was seen. The results confirm that heterogeneous population of PPR virus isolates is circulating in India which moreover emphasize the significance of molecular methods to understand the epidemiology and diversity of PPR virus in the country. The information from such studies will help in achieving the target of controlling and eradicating the disease, especially when the country is planning to launch the control programs in many states after the successful stamping out of the Rinderpest.