Information on the protistan and metazoan parasites of three species of eels, the Japanese eel Anguilla japonica, the giant mottled eel A. marmorata and the European eel A. anguilla, in Japan is summarized in the Parasite-Host List and Host-Parasite lists, based on the literature published for 93 years between 1915 and 2007. Both A. japonica and A. marmorata are native to Japan, whereas A. anguilla is an introduced species from Europe. The parasites, including 44 named species and those not identified to species level, are listed by higher taxon as follows: Sarcomastigophora (no named species), Ciliophora (6), Microspora (1), Myxozoa (6), Trematoda (7), Monogenea (7), Cestoda (3), Nematoda (7), Acanthocephala (4), Hirudinida (2), and Copepoda (1). 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 eels; 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. Of the 44 named species of parasites, 43 are from A. japonica, 1 from A. marmorata, and 10 from A. anguilla. Gyrodactylus anguillae (Monogenea) and Raphidascaris acus (Nematoda) are the exotic species that were probably introduced on A. anguilla from Europe, and it has also been suggested that G. nipponensis (Monogenea) was introduced on eels imported from somewhere in the Indo-western Pacific. Of the parasites recorded from A. japonica, eight species are marine and/or brackish-water species, of which two (i.e., Tubulovesicula anguillae, Pseudodactylogyrus kamegaii) are host-specific and occur as adults. This indicates that A. japonica serves as the definitive host for these parasites in marine and/or brackish waters where the host species constatntly remains.