Phylogenetic studies of the emergence and spread of natural recombinants in herpesviruses infecting humans and animals have been reported recently. However, despite an ever-increasing amount of evidence of recombination in herpesvirus history, the recombination process and the consequences on the genetic diversity of the progeny remain poorly characterized. We addressed this issue by using multiple single-nucleotide polymorphisms (SNPs) differentiating the two subtypes of an alphaherpesvirus, bovine herpesvirus 1 (BoHV-1). Analysis of a large sample of progeny virions obtained in a single growth cycle of coinfected BoHV-1 strains provided a prospective investigation of the recombination dynamics by using SNPs as recombination markers. We found that the simultaneous infection with two closely related herpesviruses results in a highly diversified recombination mosaic. From the analysis of multiple recombinants arising in the progeny, we provide the first evidence of genetic interference influencing the recombination process in herpesviruses. In addition, we report striking differences in the levels of recombination frequency observed along the BoHV-1 genome. With particular emphasis on the genetic structure of a progeny virus population rising in vitro, our data show to which extent recombination participates to the genetic diversification of herpesviruses.Genetic variation within a species arises through the process of mutation. If the mutation is nonlethal and if the new variant is not lost, genetic, demographic, and evolutionary processes determine its population frequency and its nonrandom association (linkage disequilibrium) with adjacent sites along the DNA segment on which it arose. Recombination is the primary genetic process that influences linkage disequilibrium over time, enabling the creation of new combinations of genetic material through the pairing and shuffling of related DNA sequences (2). In contrast with most RNA viruses, DNA replication in herpesviruses leads to rare spontaneous mutations because of an efficient proofreading activity of the DNA polymerase (6,9,10,26). With regard to the low rate of nucleotide substitution, recombination can be seen as an evolutionary driving force increasing the probability of a rare nonsynonymous mutation spreading within a herpesvirus species (44,45). In accordance with this hypothesis, recently reported phylogenetic evidence demonstrated both the high degree of gene conservation in natural herpesvirus populations and the emergence and spread of several natural recombinants in herpesvirus species that infect humans (1,24,25,29,(33)(34)(35)37) and animals (8,18,36).