Sheep pox virus (SPPV) and goat pox virus (GTPV) are classified as causing notifiable viral diseases. They belong to the genus Capripoxvirus (CaPV) along with the lumpy skin disease virus (LSDV). CaPVs are mainly host-specific, but there are frequent cross-species infections. Six strains of CaPVs were identified in outbreaks of sheep pox and goat pox in Saudi Arabia between 2013 and 2017. We investigated the sequencing features and phylogenetic analyses of the P32, PRO30 and GPCR genes of the detected SPPVs and GTPV to expose their genetic relationship. Sequence analysis revealed that the percentage of nucleotide identity of P32, PRO30 and GPCR ranged from 94% to 99%, 93% to100% and 90% to 99%, respectively, with other worldwide isolates of CaPVs. The three constructed phylogenetic trees classified the six detected CaPVs into five SPPVs and one GTPV. This study is the first to investigate the genetic relatedness among SPPVs and GTPVs based on full-nucleotide sequences of the P32, PRO30 and GPCR genes. Multiple genetic sequencing analyses and alignments will greatly improve the accuracy of the diagnosis, epidemiologic knowledge and control of CaPV diseases in Saudi Arabia.