The usefulness of the control region of mtDNA as a tool for the study of population structure in the mosquito Aedes aegypti (L.) was analyzed. Population samples were taken from several geographic areas of Argentina; one additional sample from the city of San Juan, Puerto Rico, was included for comparison. In individual mosquitoes, the A T-rich and the COII-COIII regions were amplified by polymerase chain reaction using universal insect primers. Restriction fragment-length polymorphisms were investigated from amplification products. In the A T region, three amplified fragments of different total length were obtained (of ≈2,500, 2,300, and 2,100 bp). The enzymes Ssp I, Dra I, Pac I, and Apo I produced polymorphic patterns. Including total fragment length as a variable, eight different haplotypes were resolved for Argentinian populations, some presenting a restricted geographic distribution. The coding COII-COIII region revealed very low polymorphism. Although 11 restriction enzymes were employed to analyze this region, only two different haplotypes were found, one of them shared by populations as distant as Buenos Aires and San Juan. We demonstrated that total length and restriction fragment-length polymorphisms within the noncoding A T-rich region, but not the coding COII-COIII fragment, are informative to discriminate Aedes aegypti populations. Mean F_ST value (0.48, P < 0.001) indicates an important degree of differentiation among populations. Absence of an isolation by distance pattern was demonstrated.