Although some molecular epidemiological surveys on avian haemosporidian protozoa have been conducted in Turkey, it is of great importance to increase the number of studies on the subject in this country, which has important bird migration routes between Europe and Africa. Hatay province, which is the intersection point of many bird migration routes in the intercontinental crossing, is a very suitable geographical location for the investigation of avian haemosporidian protozoa in a wide variety of bird species that use it as a route. Therefore, this study was planned to survey Haemoproteus spp., Plasmodium spp., and Leucocytozoon spp. in migratory birds sampled from this province. The animal material of the study consisted of Ciconia ciconia (Ciconiformes, n:45), Ichthyaetus melanocephalus (Charadriiformes, n:2), Pelecanus onocrotalus (Pelecaniformes, n:5) and Pelecanus crispus (Pelecaniformes, n:1). Microscopic examinations revealed Haemoproteus spp. gametocytes (5.66%) in one white stork and two Mediterranean gulls. On the other hand, nested PCR assay targeting the mitochondrial cytochrome b (Cytb) gene revealed the presence of Plasmodium/Haemoproteus spp. in 11.3% (6/53) of migratory birds. Leucocytozoon spp. was not detected by either microscopy or PCR. PCR-positive products were sequenced bi-directionally, and the GenBank and MalAvi databases were used for phylogenetic analysis and lineage identification of the isolates. This study revealed H-MYCAME08 lineage (OR227579, OR227580, OR227581, OR227582) in Ciconia ciconia and H-LARCRA01 [H. (Parahaemoproteus) larae] lineage (OR227577, OR227578) in Ichthyaetus melanocephalus, respectively. There are no studies investigating the haemosporidian parasites of these birds in Turkey, and studies on haemosporidian parasites of these species in different countries are also limited. Although the Haemoproteus MYCAME08 Cytb lineage has been demonstrated in ciconiform birds (Ciconidae) and the LARCRA01 lineage in charadriiform birds (Laridae), this study is unique in terms of reporting these lineages in different species in the same families. Inspired by this, we envisage that the expanding host range of Cytb lineages of haemosporidian protozoa is an indication that there is still a long way to go with avian haemosporidian protozoa.