While reproductive caste in eusocial insects is usually determined by environmental factors, in some populations of the harvester ants, Pogonomyrmex barbatus and P. rugosus, caste has been shown to have a strong genetic component. This system of genetic caste determination (GCD) is characterized by between-caste nuclear variation and high levels of mitochondrial haplotype variation between alternative maternal lineages. Two previous genetic models, involving a single nuclear caste-determining locus or interactions between two nuclear loci, respectively, have been proposed to explain the GCD system. We propose a new model based on interactions between nuclear and mitochondrial genes that can better explain the co-maintenance of distinct nuclear and mitochondrial lineages. In our model, females with coevolved cyto-nuclear gene complexes, derived from intra-lineage mating, develop into gynes, while females with disrupted cyto-nuclear complexes, derived from inter-lineage mating, develop into workers. Both haplodiploidy and inbreeding facilitate the buildup of such coevolved cyto-nuclear complexes within lineages. In addition, the opportunity for both intra-lineage and inter-lineage mating in polyandrous populations facilitates the accumulation of gyne-biasing genes. This model may also help to explain the evolution of workerless social, parasites. We discuss similarities of GCD and cytoplasmic male sterility in plants and how worker production of males would affect the stability of GCD. Finally, we propose experiments and observations that might help resolve the origin and maintenance of this unusual system of caste determination.