An integrative approach to managing host-parasite interactions that threaten species communities will benefit from identifying variation in parasite impact across host species, and host-parasite responses to annual climatic variation. We examine interannual, inter- and intraspecific variation in Philornis downsi intensity - an introduced blood sucking fly that causes high fitness costs in Darwin's finches on the Galápagos Islands. We sampled 131 nests of six finch species (with nestling survival ≥6 days post-hatching) between 1998 and 2005 on Santa Cruz Island. P. downsi total (per nest) and mean (per nestling) intensity differed across species and years. The woodpecker finch (Cactospiza pallida), and the large tree finch (Camarhynchus psittacula) had the highest total parasite intensity. Both species had comparatively large adult body mass, and we found a positive association between adult body mass and total parasite intensity among nestlings. P. downsi total and mean intensity was highest during the El Niño year of 1998. Surprisingly, despite a threefold difference in rainfall across lowland and highland habitats in other than the El Niño year, there was no difference in parasite intensity per nest between habitats. However, species composition of hosts and intraspecific brood size vary across habitats. Highland nests with larger broods and lower mean (per nestling) parasite intensity had higher fledging success. There was no significant effect of total parasite intensity on fledging success for intraspecific analyses. The percentage of nests with nestling mortality in each habitat ranged between 40% and 100% for all six host species.