We report the isolation of microsatellites from an enriched library of genomic repeated sequences, using a biotin-labeled oligonucleotide bound to streptavidin-coated magnetic particles. Four microsatellites were obtained from a partial library of 120 recombinant clones. This more efficient and rapid method to obtain these specific repeated sequences is preferred to the conventional isolation procedure based on the construction of a genomic library. Microsatellite markers would be promising molecular tools for the study of genetic variability of mosquito populations. Analyses of genetic structure and gene flow would provide information on the distance, direction and rate of dispersal of genes in Aedes aegypti populations. Knowledge on gene dispersal patterns is required to develop vector control strategies.