House Sparrows (Passer domesticus) are ubiquitous wild birds and can be potential reservoirs of avian haemosporidians (vector-borne blood parasites) in their habitat. The Zagros Mountain range in western Iran is an important habitat of many endangered birds. To investigate the occurrence and molecular characterization of Haemoproteus and Plasmodium spp. in Kuhdasht County in the central western region of Zagros, blood samples from 60 House Sparrows were screened by microscopic examination and PCR. An overall prevalence of 6.6%, with a varied intensity of infection (1–198 parasites per 15,000 erythrocytes) for Haemoproteus spp. and no infection for Plasmodium spp., was observed by microscopy. One of the studied cytochrome b sequences was identical to the lineage PAHIS1, and the other sequence was a new lineage, PADOM41; both were extremely similar to Haemoproteus passeris. This is the first report on the molecular detection and characterization of Haemoproteus in passerines of Kuhdasht.