In general, our understanding of Archaea lags far behind our knowledge of the other two domains of life—Bacteria and Eukarya. Unlike the other domains of life, very few viruses of Archaea have been characterized. Of the approximately 4000 viruses described to date, only 36 are associated with archaeal hosts—many of these from thermophilic Crenarchaeota. In this work we describe the discovery, isolation, and preliminary characterization of viruses and novel virus-like particles isolated directly from diverse thermal environments in Yellowstone National Park. In addition, total environmental DNA extracted from three distinct locations is used to assess the diversity of the resident archaeal community and to evaluate the diversity of thermophilic viruses. The unprecedented diversity of thermal features (~10,000) in Yellowstone National Park has provided us the opportunity to assess host and virus diversity within a single site and among geographically separated sites with distinct geochemical signatures.