At least half of all insect species carry maternally inheritedWolbachiaalphaproteobacteria, makingWolbachiathe most common endosymbionts in nature.Wolbachiaspread to high frequencies is often due to cytoplasmic incompatibility (CI), aWolbachia-induced sperm modification that kills embryos withoutWolbachia. Several CI-causingWolbachiavariants, includingwMel fromDrosophila melanogaster, also block viruses. Establishing pathogen-blockingwMel in naturalAedes aegyptimosquito populations has reduced dengue disease incidence, with one study reporting about 85% reduction whenwMel frequency is high. However,wMel transinfection establishment is challenging in many environments, highlighting the importance of identifying CI-causingWolbachiavariants that stably persist in diverse hosts and habitats. We demonstrate thatwMel-like variants have naturally established in widely distributed holometabolous dipteran and hymenopteran insects that diverged approximately 350 million years ago, withwMel variants spreading rapidly among these hosts over only the last 100,000 years.Wolbachiagenomes contain prophages that encode CI-causing operons (cifs). Thesecifsmove amongWolbachiagenomes – with and without prophages – even more rapidly thanWolbachiamove among insect hosts. Our results shed light on how rapid host switching and horizontal gene transfer contribute toWolbachiaandcifdiversity in nature. The diversewMel variants we report here from hosts present in different climates offer many new options for broadeningWolbachia-based biocontrol of diseases and pests.Significance StatementWolbachiabacteria transinfected intoAedes aegyptimosquitoes (in particular thewMelWolbachiastrain) are being widely released to suppress the transmission of dengue and other insect-vectored arboviruses. The bacterial strainwMel originated fromDrosophila melanogaster, but very little is known about its distribution and spread to other drosophilids and distantly related insects. Here we show that there has been a rapid rate of spread ofWolbachiastrains closely related towMel not just into other flies but also into wasps, indicating a large pool ofwMel variants that can be employed in vector-borne disease control.Wolbachiaprophage genes essential to this spread have evolved particularly rapidly.