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We report an analysis of seven microsatellite loci in eight populations of Anopheles maculatus mosquitoes dispersed over a distance of approximately 1,100 km in Thailand. A wide spectrum of genetic variability, with mean heterozygosities ranging from 0.738 to 0.847 were found. Based on microsatellite analysis, geographic populations of An. maculatus can be grouped into two clusters; one includes upper and lower northern populations that extend from approximately 11 degrees to 16 degrees north latitude, and the other (southern populations) extends south from about 7 degrees to 6 degrees north latitude. Wright's F(ST) and Slatkins's R(ST) for all seven microsatellite loci indicated low estimates of differentiation among all populations (mean values of F(ST) and R(ST) = 0.0406 and 0.051, respectively, corresponding to the Nm values of 5.91 and 4.65, respectively), and suggested that gene flow occurs among populations. However, there is some restriction of gene flow between the northern and southern populations. Geographic barriers could be limiting factors for greater gene flow between populations.