A methodological strategy for teaching in health and environment is to know the genetics of an important vector of dengue in different populations of mosquitoes. The aim of this study was to investigate the genetic variability of Aedes aegypti through molecular markers of mitochondrial DNA, COI, ND4 and ND5. Mosquitoes were collected using ovitraps to capture them at points located in four municipalities in the state of Mato Grosso. Subsequently, we amplified 169 samples with the best DNA result using primers for mitochondrial DNA (mtDNA): Cytochrome Oxidase Subunit I (COI - F and R), Nicotinamide Adenine Dinucleotide Dehydrogenase Subunit 4 (ND4 - F and R) and Nicotinamide Adenine Dehydrogenase 5 (ND5 - F and R). We used the Geneious software to build dendrograms for differentiating populations from each municipality. The interpopulational genetic distance obtained from sequence analysis showed a difference within populations through groups' formation in the ordering. Besides, we identified a difference in the interindividual genetic distance values, notably for the ND5 gene from the populations captured in the four municipalities. We recorded the smallest interindividual genetic distance within populations for populations from Chapada dos Guimarães. Extrinsic factors, including breeding habitat removal, can contribute to decreasing variability, consequently, the dendrogram showed some similarities. Scientific knowledge, laboratory teaching and genetic flow investigation stimulate actions to prevent transmitted diseases and support essential and effective measures to control and combat Ae. aegypti.