The rate of evolution depends on the strength of selection, which may be particularly strong for introduced parasites and their naive hosts. Because natural selection acts on phenotypes and because parasites can alter host phenotype, one fruitful starting point to measure the impact of novel pathogens is to quantify parasite-induced changes to host phenotype. Our study system is Darwin's finches on Floreana Island, Galápagos Archipelago, and the virulent fly larvae of Philornis downsi that were first discovered in Darwin's finch nests in 1997. We use an experimental approach and measure host phenotype in parasitized and parasite-free chicks in Darwin's small ground finch (Geospiza fuliginosa). Beak size did not differ between the two treatment groups, but naris size was 106% larger in parasitized chicks (~3.3 mm) versus parasite-free chicks (~1.6 mm). To test if P. downsi was present prior to the 1960s, we compared naris size in historical (1899-1962) and contemporary birds (2004-2014) on Floreana Island in small ground finches (G. fuliginosa) and medium tree finches (Camarhynchus pauper). Contemporary Darwin's finches had significantly larger naris size (including extreme deformation), whereas historical naris size was both smaller and less variable. These findings provide the first longitudinal analysis for the extent of P. downsi-induced change to host naris size and show that Darwin's finches, prior to the 1960s, were not malformed. Thus natural selection on altered host phenotype as a consequence of P. downsi parasitism appears to be contemporary and novel.