Wolbachia are being used to reduce dengue transmission by Aedes aegypti mosquitoes around the world. To date releases have mostly involved Wolbachia strains with limited fitness effects but strains with larger fitness costs could be used to suppress mosquito populations. However, such infections are expected to evolve towards decreased deleterious effects. Here we investigate potential evolutionary changes in the wMelPop infection transferred from Drosophila melanogaster to Aedes aegypti more than ten years (~120 generations) ago. We show that most deleterious effects of this infection have persisted despite strong selection to ameliorate them. The wMelPop infection is difficult to maintain in laboratory colonies, likely due to the persistent deleterious effects coupled with occasional maternal transmission leakage. Furthermore, female mosquitoes can be scored incorrectly as infected due to transmission of Wolbachia through mating. Infection loss in colonies was not associated with evolutionary changes in the nuclear background. These findings suggest that Wolbachia transinfections with deleterious effects may have stable phenotypes which could ensure their long-term effectiveness if released in natural populations to reduce population size.Author summaryMosquitoes infected with Wolbachia bacteria are being deployed into the field where they can suppress mosquito populations and reduce dengue transmission. These programs rely on the use of Wolbachia strains that have desirable phenotypes, which can include deleterious fitness effects, reproductive manipulation and virus blocking. However, theory predicts that Wolbachia will evolve to become less costly to their hosts, reducing the effectiveness of these programs. We investigate the potential for evolutionary changes by performing a comprehensive phenotypic analysis of a deleterious Wolbachia strain, wMelPop, that was introduced to Aedes aegypti mosquitoes from Drosophila over ten years ago. In contrast to theoretical expectations and research from Drosophila, our results suggest that Wolbachia strains with deleterious effects may have stable phenotypes, ensuring their long-term effectiveness if released into natural populations.