Information on the protistan and metazoan parasites of medaka, Oryzias latipes (Temminck and Schlegel, 1846), from Japan is summarized based on the literature published for 89 years between 1929 and 2017. This is a revised and updated checklist of the parasites of medaka published in Japanese in 2012. The parasites, including 27 nominal species and those not identified to species level, are listed by higher taxa as follows: Ciliophora (no. of nominal species: 6), Cestoda (1), Monogenea (1), Trematoda (9), Nematoda (3), Bivalvia (5), Acari (0), Copepoda (1), and Branchiura (1). For each parasite species listed, the following information is given: its currently recognized scientific name, any original combination, synonym(s), or other previous identification used for the parasite from medaka; site(s) of infection within or on the host; known geographical distribution in Japanese waters; and the published source of each record. A skin monogenean, Gyrodatylus sp., has been encountered in research facilities and can be regarded as one of the most important parasites of laboratory-reared medaka in Japan.