The degree to which avian haemosporidian parasites can exploit different vectors as a definitive host has ecological implications for their transmission and biogeography. Studies targeting haemosporidian parasites using precise molecular detection methods are almost lacking in Central Europe, however. Here, we utilized PCR-based molecular methods to detect avian haemosporidians in insect vectors in the Czech Republic. Nine lineages of parasites belonging to three genera, Haemoproteus, Plasmodium, and Leucocytozoon, were detected in pooled samples of insect individuals, of which three lineages had not yet been discovered in previous studies. All three Leucocytozoon lineages were found exclusively in black flies, while five Haemoproteus lineages were found in biting midges. The most abundant insect species Culicoides kibunensis harbored three Haemoproteus lineages, and the second-most numerous species Culicoides segnis even four. The positive mosquitoes of Culex pipiens complex hosted two parasite lineages, one Plasmodium and one Haemoproteus, the latter of which, however, could suggest the aberrant development of this parasite in an unusual invertebrate host. The co-occurrence of Haemoproteus ROFI1 and TURDUS2 lineages in both insects and birds at the same study plot suggests a transmission of these lineages during breeding season of birds.