Recent developments in molecular biology shed light on cross-species transmission of SPPV and GTPV. The present study was planned to characterize the capripoxviruses which were circulating in the field condition among sheep and goats using RPO30 gene-based viral lineage (SPPV/GTPV) differentiating PCR and sequencing of RPO30 and GPCR genes from clinical samples. Out of 58 scabs (35 sheep and 23 goats) screened, 27 sheep and 18 goat scabs were found positive for capripox virus infections. With the exception of one sheep and one goat scabs, all the positive samples yielded amplicon size according to host origin, i.e. SPPV in sheep and GTPV in goats. In the above two exceptional cases, goat scab and sheep scab yielded amplicon size as that of SPPV and GTPV, respectively. Further, sequencing and phylogenetic analyses of complete ORFs of RPO30 and GPCR genes from six sheep and three goat scabs revealed that with the exception of above two samples, all had host-specific signatures and clustered according to their host origin. In case of cross-species infecting samples, sheep scab possessed GTPV-like signatures and goat scab possessed SPPV-like signatures. Our study identifies the circulation of cross-infecting SPPV and GTPV in the field and warrants the development of single-strain vaccine which can protect the animals from both sheeppox and goatpox diseases.