Sheeppox virus (SPV) and goatpox virus (GPV) belong to the capripoxvirus genus of Poxviridae family. Sheeppox and goatpox along with contagious ecthyma (CE) are endemic diseases in Iran. Capripox laboratory conformation based on virological and serological techniques are time consuming, laborious and most of them of low specificity, because of close antigenic relationship between capripoxvirus and parapoxvirus. The aim of this study was to develop a capripoxvirus specific PCR assay for SPV & GPV identification on the basis of 390 bp fragment of P32 gene encoding capripoxvirus immunodominant antigen. PCR reaction was optimized using two reference strains of SPV & GPV and four field isolates in tissue culture supernatants. The identity of PCR product was confirmed by sequence analysis and the sensitivity of PCR was performed with 10 fold serial dilutions genomic LK cell DNA infected with capripoxvirus. This PCR was carried out on Twenty-nine biopsy samples from different organs of sheep and goats suspected to SPV & GPV against six biopsy samples infected with CE . Twenty-five SPV & GPV samples were positive and all of CE samples were negative. This PCR assay showed high sensitivity in detection of capripoxvirus DNA and good specificity in differentiation of capripoxvirus from parapoxvirus.