Four populations of Aedes aegypti from Manaus were studied, using allozymes and RAPD loci, to determine intra- and interpopulation genetic variability and differentiation and to compare genetic structure parameters assessed with both markers. Five RAPD primers produced 52 polymorphic fragments, whereas only seven of 18 isozyme loci were polymorphic. The population from Praça 14 was the most polymorphic (P= 94.23% and P= 55.6%); while those from Coroado (P= 82.69% and P= 44.40%) and from Cidade Nova (P= 84.61% and P= 44.40%) were the least polymorphic, for both RAPD and isozymes respectively. The observed heterozygosity was higher between populations (Ho= 0.33 – 0.38) as assessed by RAPD. Wright’s F statistics showed an Fis value higher than Fst (Fis = 0.164 > Fst = 0.048). AMOVA indicated that 95.12% of the genetic variability is intrapopulational. Even so, both of the genetic markers evaluated showed a relatively high gene flow ((Nm= 15.15), and possibly are still random couplings, although the Fis value was not low. The genetic distance between populations was similarly low for both markers: RAPD (0.012 – 0.016) and Isozymes (0.003 – 0.016). These results show that as assessed by both markers, the populations are genetically similar, and that isozymes (codominant) are the most efficient to detect the population genetic structure. Although isozymes revealed less genetic diversity than RAPDs, the estimated levels of genetic distance were identical.