The ayu or sweetfish Plecoglossus altivelis altivelis is distributed in many rivers and some lakes in Japan and also occurs in rivers of the Korean Peninsula and along the east coast of China and northern Vietnam. In Japan, this species is one of the most important freshwater fishes for commercial fisheries, aquaculture, and recreational fishing. In the present paper, information on the protistan and metazoan parasites of ayu in Japan is compiled based on the literature published for 96 years between 1912 and 2007, and the parasites, including 29 named species and those not identified to species level, are listed by higher taxon as follows: Ciliophora (no named species), Microspora (1), Myxozoa (1), Trematoda (13), Monogenea (3), Cestoda (1), Nematoda (1), Acanthocephala (3), Copepoda (4), and Branchiura (2). For each taxon of parasite, the following information is given: its currently recognized scientific name, any original combination, synonym(s), or other previous identification used for the parasite occurring in ayu; habitat (freshwater, brackish, or marine); site(s) of infection within or on the host; known geographical distribution in Japanese waters; and the published source of each locality record. There has been no record of parasites from a subspecies of ayu, the ryukyu-ayu Plecoglossus altivelis ryukyuensis. The myxozoan Mitraspora plecoglossi Fujita is transferred to the genus Hoferellus (as H. plecoglossi n. comb.), Acanthocephalus opsariichthydis Yamaguti, 1935 is determined to be the nomenclaturally correct spelling and date of that acanthocephalan species, and synonymy of the acanthocephalan Echinorhynchus oblitus Golvan with E. cotti Yamaguti is formally accepted.