Recombination contributes significantly to diversity within virus populations and ultimately to viral evolution. Here we use a recently developed statistical test to perform exploratory analysis of recombination in fourteen feline immunodeficiency virus (FIVpco) genomes derived from a wild population of cougars. We use both the global and local Phi statistical test as an overall guide to predict where recombination may have occurred. Further analyses, including similarity plots and phylogenetic incongruence tests, confirmed that three FIVpco lineages were derived from recombinant events. Interestingly, the regions of mosaic origin were clustered in the area encoding lentiviral accessory genes and largely spared the viral structural genes. Because some of the mosaic strains are currently geographically disparate, our data indicate that the dispersal of cougars infected with these strains was preceded by recombination events. These results suggest that recombination has played an important role in the evolution of FIVpco for this wild population of cougars.