The wMel and wAlbB strains of the bacterial endosymbiont Wolbachia are being introgressed into Aedes aegypti populations as a biocontrol method to reduce the transmission of medically important arboviruses. Successful introgression of Wolbachia relies on both persistence of Wolbachia throughout the host life cycle and a high fidelity of maternal transmission of Wolbachia between generations. wMel has been introgressed into field populations in 14 countries to date. Monitoring of field sites has shown that wMel prevalence can fluctuate substantially over time, prompting concerns this could lead to reduced efficacy of the biocontrol method. To explore the fidelity of wMel persistence and transmission, we developed molecular methods to measure the prevalence of Ae. aegypti negative for Wolbachia infection but carrying the “founder” mitochondrial haplotype of the single female first transinfected. As all released wMel-infected mosquitoes and any subsequent offspring will carry this founder mitochondrial haplotype, any mosquitoes with this mitochondrial haplotype and without wMel indicate that wMel was lost from this lineage at some point. We observed loss of wMel ranging from 0 to 20.4% measured at various time intervals after wMel-infected mosquito releases in five different countries. Despite some field sites showing Wolbachia loss, overall Wolbachia prevalence was sustained during the time periods studied. We then employed laboratory studies to explore factors that could contribute to the loss of wMel. Surprisingly, near-perfect maternal transmission was measured across laboratory conditions of early blood feeding, starvation, and salinity. Collectively, these findings underscore that although wMel transmission can be imperfect it does not necessarily undermine population-level establishment, providing encouragement that the intervention will be robust in most dengue-endemic environments