Parasites can play a role in speciation, by exerting different selection pressures on different host lineages, leading to reproductive barriers in regions of possible interbreeding. Hybrid zones therefore offer an ideal system to study the effect of parasites on speciation. Here, we study a hybrid zone in the foothills of the Rocky Mountains where two yellow-rumped warbler subspecies, <i>Setophaga coronata coronata</i> and <i>S. c. auduboni</i> , interbreed. There is partial reproductive isolation between them, but no evidence of strong assortative mating within the hybrid zone, suggesting the existence of a postzygotic selection against hybrids. Here, we test whether haemosporidian parasites might play a role in selecting against hybrids between <i>S. c. coronata</i> and <i>S. c. auduboni</i> . We screened birds from five transects across the hybrid zone for three phylogenetic groupings of avian haemosporidians <i>Plasmodium</i> , <i>Haemoproteus</i> and <i>Leucocytozoon</i> parasites and quantified intensity of infection. Contrary to our prediction, hybrids did not have higher haemosporidian parasite prevalence. Variation in <i>Haemoproteus</i> prevalence was best explained by an interaction between a birds' hybrid index and elevation, while the probability of infection with <i>Leucocytozoon</i> parasites was only influenced by elevation. We also found no significant difference in the diversity of haemosporidian lineages between the warbler subspecies and their hybrids. Finally, intensity of infection by <i>Haemoproteus</i> increased significantly with elevation, but was not significantly linked to birds' hybrid index. In conclusion, our data suggest that haemosporidian parasites do not seem to play a major role in selecting against hybrids in this system.