Some populations of Pogonomyrmex harvester ants comprise genetically differentiated pairs of interbreeding lineages. Queens mate with males of their own and of the alternate lineage and produce pure-lineage offspring which develop into queens and inter-lineage offspring which develop into workers. Here we tested whether such genetic caste determination is associated with costs in terms of the ability to optimally allocate resources to the production of queens and workers. During the stage of colony founding, when only workers are produced, queens laid a high proportion of pure-lineage eggs but the large majority of these eggs failed to develop. As a consequence, the number of offspring produced by incipient colonies decreased linearly with the proportion of pure-lineage eggs laid by queens. Moreover, queens of the lineage most commonly represented in a given mating flight produced more pure-lineage eggs, in line with the view that they mate randomly with the two types of males and indiscriminately use their sperm. Altogether these results predict frequency-dependent selection on pairs of lineages because queens of the more common lineage will produce more pure-lineage eggs and their colonies be less successful during the stage of colony founding, which may be an important force maintaining the coexistence of pairs of lineages within populations.