<p>In India, despite the documented presence of porcine parvoviruses (PPV1 and PPV3), only a limited number of studies reveal the genetic and evolutionary characteristics of PPV1, with no report on PPV3 genetic analysis. The VP2 protein, which plays a pivotal role as a critical antigenic domain and encodes the structural capsid protein of PPVs, serves as the focal point in this investigation. We delved into the genetic characterization of highly immunogenic VP2 gene fragments in 84 samples for PPV1 and PPV3 isolates, which were found to have a prevalence of 14.28% and 7.14%, respectively. However, 2.38% of the samples were found co-infected with PPV1 and PPV3 isolates. VP2 gene fragment from Indian PPV1 isolates had 96.38% to 98.55% sequence identity with known PPV1 isolates. On the other hand, VP2 gene fragments from Indian PPV3 isolates had 82.45% to 84.64% sequence identities with known PPV3 isolates. Phylogenetic analysis revealed that the immunogenic VP2 gene fragments of PPV3 isolates exhibited closer genetic relatedness with Asian isolates. VP2 gene fragments of Indian PPV1 and PPV3 isolates were found under positive selection pressure, which might have helped them in survival and prevalence. Further, predicted T-cell and B-cell epitope peptides in the VP2 protein fragments of PPV1 and PPV3 could help in multi-epitope-based diagnostics and vaccine development.</p>