Avian blood parasites have been intensively studied using morphological methods with limited information on their host specificity and species taxonomic status. Now the analysis of gene sequences, especially the mitochondrial cytochrome b (mt-cytb) gene of the avian haemosporidian species of Plasmodium, Haemoproteus, Fallisia and Leucocytozoon, offers a new tool to review the parasite specificity and status. The material of this study was a Tawny Owl (Strix aluco) which brought to an animal hospital with broken wings in Mugla province. Meanwhile blood smears were prepared from peripheral blood sample which was taken from the wing vein. Blood sample for genetic analyses was obtained by brachial venipuncture and genomic DNA extraction was conducted. The extracted genomic DNA was analyzed by Nested Polymerase Chain Reaction (PCR) for the amplification of partial avian haemosporidian mt-cytb gene. The final PCR product was gel purified and sequenced. The obtained isolate was deposited in GenBank International Nucleotide Sequence Database with the accession number JQ768232. Intraerytrocytic stages of Haemoproteus sp. were detected in the examination of the blood smears. The phylogenetic analyses of the amplified sequence confirmed that the owl was infected with Haemoproteus sp. According to the phylogenetic comparisons the Haemoproteus lineage showed the highest identity (99.8%) with the "H-STAL2" lineage isolated from an owl (Strix aluco) in Germany among the Haemoproteus lineages available in GenBank. In conclusion, this study reports the first microscopic and molecular detection of Haemoproteus infection in an owl in Turkey. The lineage characteristics and phylogenetic relationships among several Haemoproteus lineages were also evaluated in this study.