Insecticide intervention is still the major vector control tool of South Africa. However, despite low levels of resistance, it is notable that low levels of resistance have been detected in two of the country’s endemic provinces, KwaZulu-Natal and Mpumalanga. Currently, no increased levels of detoxification enzyme activity have been detected in adults from either province. However, survivors of insecticide exposure have been detected. To determine whether gut microbiota could potentially play a role in this survivorship, the gut microbial composition of survivors from both provinces was compared to unexposed controls of F1 Anopheles arabiensis, the major malaria vector of South Africa. Deltamethrin, permethrin and bendiocarb survivors were examined from KwaZulu-Natal and deltamethrin survivors were examined from Mpumalanga. There were both notable similarities and differences in the provinces. While untreated samples had the most unique species in Mpumalanga, more unique species were recorded after deltamethrin and bendiocarb exposure in KwaZulu-Natal. Asaia was the dominant genus in KwaZulu-Natal, regardless of treatment. There was a marked reduction in Pseudomonas in all survivors. In this province, the number of differentially abundant genera was reduced after permethrin exposure but increased after deltamethrin and bendiocarb exposure. In Mpumalanga, Asaia and Rhanella were the dominant genera, with Asaia dominating in the deltamethrin treatments. There was less of a change in differential abundance in Mpumalanga, with only Klebsiella and Asaia differentially abundant after deltamethrin exposure. These findings highlight different microbial responses in the provinces, with variable region differences. The dominance of Asaia in both provinces, particularly after deltamethrin exposure, is notable. This genus is associated with both pyrethroid resistance and reduced Plasmodium transmission. These findings suggest a potential selection for microbial resistance in both provinces. This could also underlie disease transmission patterns in South Africa, with the potential for leveraging this information for future paratransgenesis interventions.