We examined heterozygosity at hypervariable microsatellite loci and blood parasite presence—absence in five populations of Golden-winged Warblers (Vermivora chrysoptera) that span the species' Canadian range. All populations were predominantly composed of genetically pure individuals, with small proportions of phenotypic and genetic hybrids. By comparing heterozygosity and infection status in concert, we tested whether more-heterozygous individuals have lower parasite prevalence, perhaps because they possess a more robust immune system. By considering the genetic status (pure vs. hybrid) of individuals in relation to infection by parasites and heterozygosity, we build on existing research that examines the effect of Blue-winged Warbler (V. cyanoptera) hybridization on Golden-winged Warbler populations. Finally, by looking at populations across the east—west range of the species, we could hypothesize what role geographic variation in vectors might play in population-level infection rates. We found no difference in infection probability between pure and hybrid individuals, but a greater frequency of infection in populations in the western portion of the range. Our results add to the growing evidence that hybrids in this system do not face postzygotic selection, and that Golden-winged Warblers breeding in the most northwestern extent of their range may face challenges that could impede their conservation. Ongoing work that compares reproductive success of Ontario and Manitoba populations is likely to add an important dimension to our findings and could further inform conservation efforts for the species.