Flowers of the alpine skypilot, Polemonium viscosum, are attacked by nectar thieving ants of Formica neorufibarbus gelida. Ants exert selection on flower scent, size and shape in skypilots by damaging the pistils. Here, I report on the frequency and nature of contact between ants and pollen-bearing anthers and determine the consequences of such contact for pollen performance and pollen donor paternity. In laboratory trials, ants entered flowers with full intact anthers and emasculated (female) flowers equivalently. Similarly, flower visitation rates of ants foraging naturally were not affected by the frequency of male phase flowers per plant. Ants actively interacted with the pollen-bearing anthers during 21% of flower visits, on average. The rate at which such interactions occurred was predicted by the proportion of flowers in the male phase, under a random foraging model. The effect of ants on pollen fertility was tested experimentally by enclosing ants in male-phase flowers on intact inflorescences. Adjacent control flowers were left un-occupied. Pollen from flowers with a history of ant occupancy had significantly lower germination on virgin recipient stigmas than pollen from unoccupied control flowers. With hand-pollination, sufficient pollen was transferred from ant-occupied flowers to saturate seed set. However, a model based on the relationship between seed set and compatible pollen delivery by natural pollinators indicated that ant damage to pollen should reduce paternity accruing per flower visit by 20–26% on average, in nature. Results support the hypothesis that in P. viscosum, selection on floral traits by nectar-thieving ants operates through male as well as female function.