Avian hemosporidian parasites have been detected in Asia, but little information is known about the hemosporidian parasite lineages that circulate in waterbirds that migrate along the East Asian and Central Asian migratory flyways to breed in Mongolia. To gather baseline data on hemosporidian parasite presence in Mongolian waterbirds, 151 blood-spot samples (81 hatch year [HY] and 70 after hatch year [AHY]) from Bar-headed Goose (Anser indicus), Ruddy Shelduck (Tadorna ferruginea), Great Cormorant (Phalacrocorax carbo), and Mongolian Gull (Larus mongolicus) were screened for three genera of apicomplexan parasites, Plasmodium, Haemoproteus, and Leucocytozoon, using nested PCR. Of these, 17 samples (11%, 95% confidence interval: 7.1–17.4%), representing all four species, were positive. We identified 10 species (six Plasmodium, one Haemoproteus, and three Leucocytozoon) through mitochondrial DNA sequencing of the cytochrome b gene and BLAST analysis. One lineage shared 100% nucleotide identity to a hemosporidian parasite lineage that has been previously identified as Plasmodium relictum (SGS1). Six lineages were found in AHY birds and five in HY birds, the latter confirming that infection with some of the identified hemosporidian parasites occurred on the breeding grounds. Our data provide important baseline information on hemosporidian parasite lineages found in AHY waterbirds that breed and migrate through Mongolia as well as in HY offspring.