Tephritid fruit fly pests remain a considerable problem for agricultural fruit production around the world. New control methods that do not rely on synthetic insecticides are increasingly desirable to diversify tephritid pest management programs. Biological control through the release of parasitoid wasps has historically provided effective suppression of fruit fly pests, although molecular factors that influence the success of fruit fly parasitoids are understudied. Microbes have been demonstrated to facilitate myriad interactions between insects and their environment and have been the subject of recent investigation within tephritids. Specifically, the diversity and function of viruses found within fruit flies and associated parasitoids is an emerging field of research that has the potential to deepen our understanding of previously hidden factors that facilitate sustainable pest control. Most work to date has focused on identifying resident viral communities within fruit flies using metagenomic and metatranscriptomic sequencing approaches. Additionally, a growing body of evidence has revealed a multitude of functional dynamics that viruses have with fruit fly hosts, including vertically transmitted commensal viruses and parasitoid-vectored pathogens. Heritable viruses transmitted by fruit fly parasitoids, in particular, have been shown to play prominent roles in fruit fly multitrophic interactions, in which viral infection can shape the survival rate and host range of infected parasitoids. Furthermore, at least one parasitoid virus represents a lethal pathogen to a wide range of fruit fly pest species. Parasitoid viruses could therefore present novel opportunities to leverage natural antagonistic interactions for fruit fly pest control innovations.