The Aedes aegypti mosquito serves as a vector for several diseases, including dengue, Zika, chikungunya, and yellow fever. This species is well adapted to urban environments and poses a significant threat to public health. Some studies suggest that the gut bacteria of insect vectors may play a crucial role in developing resistance to insecticides. This study assessed the resistance of Ae. aegypti from Florencia, Caquetá, to temephos and deltamethrin and analyzed the diversity of gut bacteria in resistant larvae and adult females. Larvae exhibited resistance to temephos at a lethal concentration 50 (LC50) of 0.034 µg/mL, while females showed resistance to deltamethrin at a discriminant concentration of 10 µg/mL. The bacterial load in the guts of deltamethrin-treated females (3.42 × 106 CFU/mL) was significantly higher compared to temephos-treated larvae (9.4 × 105 CFU/mL) and untreated females (8 × 104 CFU/mL). A total of sixty-eight bacterial strains were isolated from the guts of both larval and resistant females Ae. aegypti, with 31 strains identified through 16S rRNA gene analysis and 11 confirmed by gyrB gene sequencing. In untreated females, Bacillus comprised 12.55% of the gut bacteria and was identified as an exclusive genus. In resistant larvae, Serratia was the most abundant and exclusive genus, accounting for 35.29%, while in resistant females, Cedecea was the predominant genus, representing 66.67%. These findings suggest that gut bacteria may influence the resistance of Ae. aegypti to temephos and deltamethrin. Furthermore, this research provides valuable information that can be considered for the design of local vector control strategies. The results highlight new research focused on the study of insecticide tolerance and degradation within the gut microbiota of insect vectors of arboviruses.