The objective of this study was to disentangle the relative effects of Pgm-3 and Gp-9 and/or other closely linked genes on the phenotypes and reproductive success of queens in introduced (USA) populations of S. invicta. Gp-9 ora closely linked gene(s) was found to have major effects on queen weight; the likelihood that queens Shed their wings (a behaviour associated with the onset of reproduction), and the probability that queens are accepted in polygyne (multiple-queen) colonies. Our analyses show that once the effect of Gp-9 genotype is taken into account, Pgm-3 genotype no longer is significantly associated with differences in queen phenotype or the probability of queens being accepted in. polygyne colonies. This suggests that the associations of Pgm-3 genotype with weight, wing shedding rate and probability of acceptance by polygyne colonies previously reported in studies that did not control for the effects of Gp-9 are due to the strong linkage disequilibrium that exists between Pgm-3 and Gp-9, or to linkage disequilibria between these and other genes affecting queen phenotype and fitness. Several lines of evidence, including data from the native South American range, suggest that additional cryptic alleles at Gp-9, or additional genes in the same linkage group as Gp-9, must be involved in controlling queen phenotype and the large suite of traits important in determining social organization of S. invicta colonies.