Evolution is the study of how variation alters the phenotype and population dynamics over time. Population genetics theories fit viral evolution well because of the properties of a viral population. Retroviruses are characterized by a high mutation and replication rate, which produces a heterogeneous mixture of viral variants commonly referred to as a quasispecies. Equine infectious anemia virus (EIAV) infection is a well-studied model for retrovirus variation and evolution (32, 33, 34). EIAV infection is characterized by a rapid, variable, dynamic disease course. Dynamic features of clinical disease as well as the ability of the horse to control the infection makes EIAV an excellent system to study evolution of viral quasispecies during progression of clinical disease. Here, we describe analyses of genetic data from longitudinal studies of genetic variation in a horse experimentally infected with equine infectious anemia virus. These studies include the genes encoding the regulatory protein Rev and the surface envelope glycoprotein, SU.Phylogenetic and cluster analyses suggested that the population of Rev variants was comprised of two distinct quasispecies that co-existed during infection, the populations shifted rapidly during febrile and afebrile periods with as little as 10 days between changes in population dominance of populations. In this study, we also examined evolution of EIAV envelope quasispecies during chronic and inapparent stages of disease. The data suggests that viral quasispecies in the chronic period evolve by random processes while quasispecies in the inapparent period evolve by a combination of Darwinian selection and random processes. These results propose that the envelope evolves by different processes during different stages of disease. Different evolutionary mechanisms during different stages of disease require unique approaches to anti-retroviral therapy during different stages of disease. Together, these results suggest there are unique host environments and viral population interactions during different stages of disease. Multiple quasispecies and varying processes of evolution during persistent retrovirus infection challenges the current thinking and has important biological implications for control of viral infections.