We describe genetic structure at microgeographical scales in two social forms of the introduced fire ant Solenopsis invicta using nuclear and mitochondrial markers. Fire ant populations in northern Georgia, U.S.A. are structured in fundamentally different ways at the two genomes. Virtually all nuclear genetic variation resides within sampling sites; no differentiation was apparent between the social forms and only minimal differentiation was found among sites in only one social form (the polygyne form, which has nests with numerous queens). In contrast, substantial mtDNA variation exists at all levels; the forms are significantly differentiated and strong divergence was detected among sites in the polygyne form. No mtDNA differentiation was found among sites in the monogyne form (which has nests with a single queen). These results are predicted on the basis of the social biology of the ants. Monogyne queens and males of both forms presumably disperse widely, and polygyne queens commonly mate with monogyne males, thus explaining the uniformity of nuclear allele frequencies across sampling sites and between the forms. Polygyne queens display habits consistent with limited dispersal, and queens of both forms seem unable to establish themselves as reproductives in nests of the alternate form, thus explaining the strong microgeographical structure within the polygyne form and differentiation between the forms found using mtDNA markers. The mtDNA haplotypes are distributed among sites in a manner that suggests a mechanism for the spread of polygyny in introduced fire ants. Monogyne queens apparently mate occasionally with polygyne males and acquire a Mendelian nuclear factor allowing the expression of polygyny in their sexual daughters.