Significance Viruses pose enormous threats to human health around the world but can also be potential tools for everything from gene therapy to medical imaging to drug delivery. We have used cryo-electron microscopy to determine the atomic structure of two filamentous viruses that infect hosts living in some of the most extreme environments on the Earth’s surface, springs of nearly boiling acid. We show how the structure of the proteins that protect the viral DNA has been conserved in a family of filamentous viruses found in diverse extreme locations around the globe, suggesting that all had a common origin. These results have implications for understanding the evolution of viruses, as well as for developing new methods for packaging DNA in biotechnology.