Technical Abstract: We generated and analyzed microsatellite genotypic data and mtDNA sequence data from the fire ant Solenopsis invicta collected from two separate infested areas (Taoyuan and Chiayi) in Taiwan to infer the population and colony structure of these recently established populations. These genetic analyses revealed the following patterns: 1) relatedness among worker nestmates was significantly greater than zero for both social forms from both populations; 2) No significant isolation by distance was found among nests within each social form from either population; 3) Significant mtDNA but no nuclear differentiation occurs between sympatric social forms in Taoyuan; 4) Molecular signatures of genetic bottlenecks associated with recent introductions are evident in both populations; and 5) The two sampled populations, Taoyuan and Chiayi, are highly genetically differentiated at both the nuclear or mtDNA genomes and most likely derive from two separate introductions into Taiwan. While results from these analyses generally were consistent with predictions based on the known biology of these ants and similar studies of S. invicta in the U.S.A. and South America, some patterns likely reflect the recent introduction and human-mediated inadvertent transport of ants in Taiwan. This is the first study to investigate the population and colony structure of fire ants in Taiwan and results from our study represent an important contribution to the ongoing efforts aimed at eradicating this invasive pest in Taiwan.