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Background Insecticide use continues as the main strategy to control Aedes aegypti, the vector of dengue, Zika, chikungunya, and yellow fever. In the city of Tapachula, Mexico, mosquito control programs switched from pyrethroids to organophosphates for outdoor spatial spraying in 2013. Additionally, the spraying scheme switched from total coverage to focused control, prioritizing areas with higher entomological-virological risk. Five years after this strategy had been implemented, we evaluated the status and variability of insecticide resistance among Ae. aegypti collected at 26 sites in Tapachula. Methodology/Principal findings We determined the lethal concentrations at 50% of the tested populations (LC50) using a bottle bioassay, and then, we calculated the resistance ratio (RR) relative to the susceptible New Orleans strain. Permethrin and deltamethrin (pyrethroids), chlorpyrifos and malathion (organophosphates), and bendiocarb (carbamate) were tested. The frequencies of the substitutions V1016I and F1534C, which are in the voltage-gated sodium channel and confer knockdown-resistance (kdr) to pyrethroid insecticides, were calculated. Despite 5 years having passed since the removal of pyrethroids from the control programs, Ae. aegypti remained highly resistant to permethrin and deltamethrin (RR > 10-fold). In addition, following 5 years of chlorpyrifos use, mosquitoes at 15 of 26 sites showed moderate resistance to chlorpyrifos (5- to 10-fold), and the mosquitoes from one site were highly resistant. All sites had low resistance to malathion (< 5-fold). Resistance to bendiocarb was low at 19 sites, moderate at five, and high at two. Frequencies of the V1016I ranged from 0.16–0.71, while C1534 approached fixation at 23 sites (0.8–1). Resistance profiles and kdr allele frequencies varied across Tapachula. The variability was not associated with a spatial pattern at the scale of the sampling. Conclusion/Significance Mosquito populations respond to selection pressure at a focal scale in the field. Spatial variation across sites highlights the importance of testing multiple sites within geographical regions., Author summary Aedes aegypti is a major vector of dengue, chikungunya, Zika, and yellow fever. In the absence of effective vaccines or treatments, the suppression of mosquito populations using insecticides commonly has been implemented by public health programs. Unfortunately, few insecticides are available to target adult mosquitoes with outdoor spraying. The mismanagement of insecticides can lead to resistance selection in mosquitoes, affecting our ability to control arboviral diseases. Ideally, screening insecticide susceptibility in local mosquito populations allows public health entities to support insecticide management strategies that will prevent the development of resistance. In this study, we evaluated insecticide resistance in Ae. aegypti collected across 26 sites in Tapachula, Mexico. The results reveal the response of populations to its historic use of insecticides. High resistance to pyrethroids, used for 10 years, but not in the previous 5 years, and moderate to high resistance to chlorpyrifos, an insecticide from a different toxicological group and used for the past 5 years, were confirmed. High variation in resistance across Ae. aegypti sites suggests that focal selection plays an important role in the evolution of insecticide resistance in the field. Screening several collections sites within a geographical region provides better evidence to support strategies of insecticide management.