A population genetic analysis of gene flow was conducted among 10 Aedes aegypti collections from seven cities along the northeastern coast of Mexico. Four collections were made from Monterrey to examine local patterns of gene flow. Markers included 60 random amplified polymorphic DNA (RAPD) loci amplified by the polymerase chain reaction and single strand conformation polymorphism analysis of variation in a 387-basepair region of the NADH dehydrogenase subunit 4 from the mitochondrial DNA (mtDNA). Seven mitochondrial haplotypes were detected and phylogenetic analysis identified two well-supported clades. Regression analysis of geographic distances and pairwise FST estimated from RAPD markers indicated that populations are isolated by distance and that free gene flow occurs among collections within 90-250 km. Isolation by distance was not detected using mtDNA haplotypes. The Nuevo Laredo collection had unique RAPD and mtDNA haplotype frequencies and reduced heterozygosity suggesting that few mosquitoes established this population.