Bovine papular stomatitis virus (BPSV) infects cattle and, occupationally, humans. Prevalent subclinical infections, frequent reinfections, and virus persistence in healthy animals compound a poorly understood, but likely complex, scenario of BPSV perpetuation and transmission in nature. Here, we report the isolation of multiple BPSV strains coinfecting a single animal. Whole-genome analysis of isolated BPSV strains revealed genomic variability likely affecting virus virulence and infectivity. Further, incongruent phylogenetic relationships between viruses suggested genomic recombination. These results have significant implications for parapoxvirus infection biology and virus evolution in nature.