In 2000, Brazil reported 180,137 cases of dengue, ≈80% of the total in the Americas. However, little is known about gene flow among the vector populations in Brazil. Random amplified polymorphic DNA (RAPD) was used to study the genetic structure of Aedes aegypti in 15 populations from five states, with a range extending 2,800 km. An analysis of 47 polymorphic RAPD loci estimated gene flow at the macro- (different states) and micro- (different cities) geographical levels. Genetic polymorphism was high (H_S = 0.274), and high levels of genetic differentiation existed both between different states (G_ST = 0.317) and between cities or neighborhoods in each state (G_ST = 0.085–0.265). These values are higher than those described for any other populations of A. aegypti.