We analyzed blood samples of resident and migratory Japanese birds to evaluate the prevalence and genetic background of avian blood parasites in northern Japan. We used PCR targeting the mitochondrial cytochrome b gene to examine infections of Leucocytozoon, Haemoproteus, and Plasmodium parasites in blood samples from 243 birds of 14 species in three orders (Passeriformes, Columbiformes, and Anseriformes). Sequences were subjected to phylogenetic analysis. The infection rate was 21% in pigeons (Columbiformes) and 17% in Anseriformes. A high infection rate of 93.8% was found in crow species (Passeriformes). Haemoproteus and Plasmodium parasites were detected in only two species. Infected blood samples obtained from seven bird species involved two major clades of Leucocytozoon, which were divided between resident and migratory birds. The parasites, which are genetically distinct from parasites in Japanese resident birds, may have been introduced to Japan by migratory bird species.