Esterases are groups of enzymes that increase the mechanism of action of insect vectors in their metabolic activity while under environmental pressure. The aim of this study was to analyze the level of �-esterase expression in Aedes aegypti populations in the municipalities of Cuiabá and Várzea Grande, MT as a way to contribute to vector research. Samples were collected through ovitraps in each municipality and allele results were analyzed by factorial ANOVA between months, locations and seasonal phase. The alleles of 385 Ae. aegypti individuals demonstrated the highest expressions during the ebb period, significantly between months (F7,377=6.89; p<0.01) and between sites (F1,383=11.01). Expressed and superexpressed alleles decreased in Mar/2016, during the "peak water" period and resumed from May/2016 to Nov/2016. Regarding the frequency, expressed alleles increased in Várzea Grande, during the flood period with the highest precipitation. There was an increasing tendency of the expressed alleles with precipitation and the frequency values between Oct/2015 (30%±88) and Feb/2016 (89±55%); meanwhile, for the superexpressed alleles, this occurred during the ebb period (42±91%). Várzea Grande specimens reached a higher frequency of expressed alleles (75±41.36%), but there was a reduction of overexpressed alleles in both municipalities (F2,13=12.39; p<0.01). The results obtained in this study indicate that the esterase isoenzyme method was sensitive enough to detect variations in allele frequency in natural Ae. aegypti populations, which implies an increased metabolic activity over the period examined.