Interspecific hybridization can often impose a substantial fitness cost due to reduced hybrid viability or fecundity. In social insects, however, such costs disproportionately impact reproductive offspring, whereas hybrids who become sterile workers can be functional, and even beneficial, colony members. Genomic imprinting of the paternal genome in reproductive, but not worker female offspring has been proposed as a mechanism to avoid genomic incompatibilities in hybrid queens in a hybrid zone between two fire ant species, Solenopsis geminata and S. xyloni. A study of allozyme variation demonstrated differences between the worker caste displaying a hybrid phenotype, and the winged queen caste displaying only the mother's phenotype. In this study, we investigate whether these differences are caused by genomic imprinting or genetic differences between castes by comparing variability of proteins to that of microsatellite markers. Workers and winged queens differed genetically at both classes of marker, indicating that allozyme differences were caused by underlying genetic differences between castes rather than differences in gene expression due to imprinting. Workers were F₁ S. geminata × S. xyloni hybrids, whereas nearly all winged queens were of pure S. xyloni ancestry. Thus, S. xyloni within the hybrid zone appears to have evolved social hybridogenesis, in which the loss of worker potential in pure-species offspring necessitates hybridization for worker production, but prevents hybrids from being represented in the reproductive caste.