Herpesvirus are ancient pathogens that have co-evolved with their cognate hosts. The use of pioneering enrichment methods to sequence herpesvirus genomes directly from clinical material has revealed unexpected insights into the evolution and pathogenesis of these DNA viruses . We find that recombination is a dominant driver of herpesvirus evolution, with herpes simplex and cytomegalovirus recombining freely, other than in key hotspots. In contrast varicella zoster virus and Epstein Barr virus recombination is constrained leading to evidence of population structure. While the forces shaping the VZV and EBV population structure are unknown the data suggest possible hypotheses that will be explored. Mathematical modelling of sequence data recovered from clinical samples also provides insight into the natural history of these human-restricted viruses in their natural host, leading to new findings and testable hypotheses about pathogenesis and virulence.