Haemosporidians are a group of vector-borne parasites belonging to the order Haemosporida. They infect avian hosts and require blood-sucking insects (Diptera) for their transmission. The occurrence and diversity of haemosporidian parasites are shaped primarily by the specificity of the parasite and the susceptibility of the host/vector. In this study, the presence and distribution of haemosporidians in blood samples from birds in urbanized and natural habitats were estimated using microscopic and molecular approaches. Birds in urbanized habitats were infected with four different species of Plasmodium: Plasmodium relictum, P. vaughani, P. matutinum, P. circumflexum, two different species of Haemoproteus: Haemoproteus majoris, H. parabelopolskyi, and Leucocytozoon sp. The species, H. attenuatus, H. concavocentralis, H. minutus, H. pallidus, H. noctue and H. tartakovskyi were additionally identified in birds in natural habitats. Typically, juvenile birds are essential markers of parasite species transmitted in the study area. The juveniles in the urbanized habitats carried the P. relictum, P. vaughani, P. circumflexum, H. parabelopolskyi, H. majoris, and Leucocytozoon species. The most abundant parasite was H. parabelopolskyi, which was found in both types of habitats. The prevalence of the Haemoproteus/Plasmodium species by nested PCR in birds in natural habitats (in totally 43.80%; 53/121) was significantly higher than that in birds in urbanized habitats (in totally 21.94%; 43/196) (p < 0.05), even in spring. There was no statistically significant difference between habitat types in overall infection rate of Leucocytozoon sp. (p > 0.05; 10/121 vs. 19/196), neither overall nor in the spring.