Abstract Background Xenotransplantation may overcome significant shortage of human allotransplant. Porcine organs are considered favorable for xenotransplantation duo to similar size and function to human organ. However, porcine endogenous retroviruses (PERVs) are potential infectious agents during xenotransplantation as they are able to infect and horizontally transfer among human cells. Furthermore, PERVs can be endogenized in pig genomes and are transmitted genetically in a Mendelian fashion. Here, we depict a complex evolutionary history of modern PERVs. Results We in silico mined 142 mammalian genomes and 14 pig genomes. This led to the documentation of 185 PERVs and a new viral cluster. Large-scale genomic alterations were found in most PERVs including many insertion-deletion events and which are suggestive of ancient origins, and pig genomes have been shaped by PERV-mediated genomic rearrangement during evolution. Notably, we found that lesser Egyptian jerboa and rock hyrax harbor ancestral PERV-related elements indicative of ancient cross-species transmission events from none-porcine species to pigs. A comprehensive analysis of these viral “fossils” suggested that recombination among none-porcine endogenous retroviruses led to the origination of PERVs. Conclusion For the first time, using large scale genomic mining, we decipher a complex evolutionary history for the PERVs. These new findings help us to understand the past of PERVs which pose the potential risk in clinical trials of xenotransplantation and provide novel insights into the origin and evolution of a human-infecting pathogen.