Species of Haemoproteus (Haemosporida, Haemoproteidae) are widespread and often prevalent blood parasites of birds all over the word. They are particularly diverse in tropical countries. Due to limited knowledge of life cycles, these pathogens usually have been considered relatively benign and were neglected in veterinary medicine and bird management. However, recent molecular studies provided evidence that Haemoproteus parasites might cause severe diseases if they infect non-adapted (wrong) avian hosts due to marked damage of organs by exo-erythrocytic stages (megalomeronts). Additionally, high Haemoproteus infections are lethal to blood-sucking insects. Molecular markers are essential for reliable detection and species identification both at tissue stages in vertebrates and sporogonic stages in arthropods however, remain insufficiently developed for wildlife haemosporidian parasites. This study combined PCR-based and microscopic approaches and reported cytochrome b gene (cytb) and apicoplast gene (clpc) markers for characterization of six widespread species of haemoproteids parasitizing common birds wintering in tropics and subtropics of the Old World. Three new Haemoproteus species were described using morphological and molecular markers. Molecular characterization of haemoproteids parasitizing falcons was developed. Morphological and phylogenetic characterization of Haemoproteus tinnunculi (cytb lineage hFALSUB01), H. brachiatus (hLK03), H. parabelopolskyi (hSYAT1), H. homogeneae n. sp. (hSYAT16), H. homopicae n. sp. (hGAGLA07) and H. homominutus n. sp. (hCUKI1) was performed and provides clues for infections diagnostics. This study adds three species to the group of morphologically readily distinct Haemoproteus parasites, which differ in few base pairs (< 1%) in their partial cytb sequences, indicating that low genetic difference in such sequences often show between-species divergence and should be carefully applied in taxonomic biodiversity studies of haemosporidian parasites. Bayesian phylogenetic analysis identified the position of detected lineages in regard of other Haemoproteus species, suggesting that all reported parasites belong to subgenus Parahaemoproteus and likely are transmitted by Culicoides biting midges. Importance of clpc gene sequences was specified in haemosporidian parasite taxonomy on species levels.