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Simple Summary: Responsible for the transmission of arboviruses, the mosquito Aedes aegypti is a major challenge to public health in Brazil, particularly in urban areas located within tropical and subtropical regions. The recent epidemiological bulletins from the Brazilian Health Ministry in the state of Maranhão have reported high levels of urban infestation by this vector, which represents a potential risk for the occurrence of new epidemics. In this context, the present study describes the partial mitochondrial genome of a sample of Ae. aegypti from the Brazilian state of Maranhão. Studies of this type provide important insights into the biological evolution of this important species and have the potential to contribute to the development of increasingly effective strategies for the control of this disease vector. Aedes aegypti is a mosquito native to the African continent, which is now widespread in the tropical and subtropical regions of the world. In many regions, it represents a major challenge to public health, given its role in the cycle of transmission of important arboviruses, such as Dengue, Zika, and Chikungunya. Considering the epidemiological importance of Ae. aegypti, the present study sequenced the partial mitochondrial genome of a sample collected in the municipality of Balsas, in the Brazilian state of Maranhão, followed by High Throughput Sequencing and phylogenetic analyses. The mitochondrial sequence obtained here was 15,863 bp long, and contained 37 functional subunits (thirteen PCGs, twenty-two tRNAs and two rRNAs) in addition to a partial final portion rich in A+T. The data obtained here contribute to the enrichment of our knowledge of the taxonomy and evolutionary biology of this prominent disease vector. These findings represent an important advancement in the understanding of the characteristics of the populations of northeastern Brazil and provide valuable insights into the taxonomy and evolutionary biology of this prominent disease vector. [ABSTRACT FROM AUTHOR]