We test for fitness costs of resistance in a natural host–parasite system, involving Drosophila nigrospiracula and ectoparasitic mites, Macrocheles subbadius. We contrasted rates of mortality at embryonic and pupal stages of host ontogeny between replicate-resistant and -susceptible (control) lines at different temperatures (24, 28, and 34°C). Evidence for a cost of resistance was shown as a 17% overall reduction in egg hatch rate in replicate-resistant lines, although this effect was heterogeneous across replicate selection experiments. This cost of resistance was not magnified under thermal stress. Pupa survivorship was statistically invariant between resistant and control lines, at either temperature. Embryo and pupa mortalities were significantly elevated at the high temperature, confirming that the thermal treatment was physiologically stressful. The results suggest differential sensitivity of life history traits to the pleiotropic effects of genetic resistance against ectoparasitic mites.