Hybridisation can increase adaptive potential when enhanced genetic diversity or novel genetic combinations confer a fitness advantage, such as in the evolution of anti-parasitic mechanisms. Island systems are especially susceptible to invasive parasites due to the lack of defence mechanisms that usually coevolve in long-standing host-parasite relationships. We test if host genetic admixture affects parasite numbers in a novel host-parasite association on the Galápagos Islands. Specifically, we compare the number of Philornis downsi in nests with offspring sired by Darwin’s small tree finch (Camarhynchus parvulus), Darwin’s medium tree finch (C. pauper), and hybrids of these two species. The number of P. downsi decreased with increasing genetic admixture of the attending male, and nests of hybrid males had ~ 50 % fewer parasites than C. parvulus nests, and ~ 60 % fewer parasites than C. pauper nests. This finding indicates that hybridisation in this system could be favoured by selection and reveal a mechanism to combat an invasive parasite.