In order to establish the genetic variability of Aedes aegypti determined by the analysis of the MT-ND4 gene, in eleven endemic regions for dengue in Peru, 51 samples of Ae. Aegypti were tested. The genetic variability was determined through the amplification and sequencing of a fragment of 336 base-pairs of MT ND4, the analysis of intra-specific phylogeny was conducted with the Network Ver. 4.6.10 program; and the phylogenetic analysis, with the Neighbor Joining distance method. The presence of five haplotypes of Ae. Aegypti grouped in two lineages was identified: the first one includes haplotypes 1, 3 and 5, and the second one comprises haplotypes 2 and 4. The geographic distribution of each of the haplotypes found is also shown. It is concluded that this variability is caused by the active migration of this vector and the human activity-mediated passive migration.