The fundamental goal of population genetics is to understand the relative importance of micro evolutionary forces in determining the existence of genetic variation within a species. The variance in effective population size is an important quantity in evolutionary biology, which helps in describing the rate at genetic variance changes due to genetic drift. The fire ant represents an excellent model system to conduct detailed studies of genetic structure using many markers of multiple classes. With this rationale a study was initiated to assess genetic differences of fire ants among different places and to estimate effective population sizes in the presence of gene flow.