Publisher Summary This chapter discusses the molecular systematics of wasp and polydnavirus (PDVs) genomes and their coevolution. Polydnaviruses are integrated, inherited DNA viral endosymbionts of parasitoid wasps found within some lineages of Braconidae and Ichneumonidae that attack caterpillars (larval Lepidoptera). Due to their chromosomal integration and mode of inheritance, phylogenomic relationships among the PDVs are closely tied to phylogenetic relationships among the host wasps that carry them. We have inferred that PDVs must have at least three independent ancient origins in the wasps: bracoviruses (BVs) from ancestral nudiviruses associated with braconid wasps, ichnoviruses, and “banchoviruses” from still unidentified progenitor viruses and associated with unrelated families of Ichneumonidae. Phylogenetic studies of the BV-carrying lineage of braconid wasps are now guiding comparative studies of BV genomes and advancing our understanding of the roles that BV genes may play in the evolution of wasp/caterpillar parasitic relationships.