Creptotrematina Yamaguti, 1954 (original description)
Creptotrematina dissimilis (Teixeira de Freitas, 1941) Yamaguti, 1954 (new combination reference)
Fellodistomum magnum (Manter, 1934) Yamaguti, 1954 accepted as Steringophorus magnus Manter, 1934 (new combination reference)
Fellodistomum profundum (Manter, 1934) Yamaguti, 1954 accepted as Steringophorus profundus Manter, 1934 (new combination reference)
Genarchopsis lobata (Srivastava, 1933) Yamaguti, 1954 accepted as Genarchopsis goppo Ozaki, 1925 (new combination reference)
Genarchopsis singularis (Srivastava, 1933) Yamaguti, 1954 accepted as Genarchopsis goppo Ozaki, 1925 (new combination reference)
Genolinea argentinae Yamaguti, 1954 (original description)
Gonocercella trachinoti (MacCallum, 1913) Yamaguti, 1954 (new combination reference)
Hamacreadium palleniscum (Shipley & Hornell, 1905) Yamaguti, 1954 accepted as Neolebouria pallenisca (Shipley & Hornell, 1905) Martin, Cutmore, Ward & Cribb, 2017 accepted as Paramanteriella pallenisca (Shipley & Hornell, 1905) Martin, Cutmore & Cribb, 2017 (new combination reference)
Hurleytrematoides Yamaguti, 1954 (original description)
Hurleytrematoides chaetodoni (Manter, 1942) Yamaguti, 1954 (new combination reference)
Hypocreadium anandrum (Manter, 1947) Yamaguti, 1954 (new combination reference)
Hypocreadium spinosum (Manter, 1940) Yamaguti, 1954 (new combination reference)
Lasiotocus costaricae (Manter, 1940) Yamaguti, 1954 accepted as Alloinfundiburictus costaricae (Manter, 1940) Wee, Cutmore, Pérez-del-Olmo & Cribb, 2020 (new combination reference)
Lasiotocus longicaecum (Manter, 1940) Yamaguti, 1954 accepted as Alloinfundiburictus longicaecum (Manter, 1940) Wee, Cutmore, Pérez-del-Olmo & Cribb, 2020 (new combination reference)
Lasiotocus macrorchis (Yamaguti, 1934) Yamaguti, 1954 accepted as Paralasiotocus macrorchis (Yamaguti, 1934) Wee, Cutmore, Pérez-del-Olmo & Cribb, 2020 (new combination reference)
Lasiotocus malasi (Nagaty, 1948) Yamaguti, 1954 (new combination reference)
Lasiotocus odhneri (Srivastava, 1939) Yamaguti, 1954 (new combination reference)
Lasiotocus parvus (Manter, 1942) Yamaguti, 1954 accepted as Paralasiotocus parvus (Manter, 1942) Wee, Cutmore, Pérez-del-Olmo & Cribb, 2020 (new combination reference)
Lasiotocus plectorhynchi (Yamaguti, 1934) Yamaguti, 1954 accepted as Genolopa plectorhynchi (Yamaguti, 1934) Hopkins, 1941 (new combination reference)
Lepidauchen skrjabini (Layman, 1930) Yamaguti, 1954 (new combination reference)
Lintonium pulchrum (Johnston, 1913) Yamaguti, 1954 (new combination reference)
Metadena apharei (Yamaguti, 1942) Yamaguti, 1954 (new combination reference)
Monascus typicus (Odhner, 1911) Yamaguti, 1954 accepted as Monascus filiformis (Rudolphi, 1819) Looss, 1907 (new combination reference)
Mordvilkoviaster Pigulewsky, 1938 accepted as Aponurus Looss, 1907 (subsequent type designation)
Opechona retractilis (Lebour, 1908) Yamaguti, 1954 accepted as Opechona bacillaris (Molin, 1859) Dollfus, 1927 (new combination reference)
Opechona sebastodis (Yamaguti, 1934) Yamaguti, 1954 (new combination reference)
Opecoelus ozaki (Layman, 1930) Yamaguti, 1954 (new combination reference)
Orientocreadium hyderabadi (Dayal, 1938) Yamaguti, 1954 (new combination reference)
Paradiscogaster caranxi (Srivastava, 1939) Yamaguti, 1954 accepted as Paradiscogaster indicus (Srivastava, 1939) Cribb, Anderson & Bray, 1999 (new combination reference)
Pisciamphistoma Yamaguti, 1954 (original description)
Pisciamphistoma stunkardi (Holl, 1929) Yamaguti, 1954 (new combination reference)
Plagioporus orientalis (Yamaguti, 1934) Yamaguti, 1954 accepted as Neoplagioporus elongatus (Goto & Ozaki, 1930) Shimazu, 1990 (new combination reference)
Plagioporus truncatus (Linton, 1940) Yamaguti, 1954 accepted as Neolebouria truncata (Linton, 1940) Gibson, 1976 accepted as Trilobovarium truncatum (Linton, 1940) Martin, Cutmore & Cribb, 2017 (new combination reference)
Plagioporus zacconis (Yamaguti, 1934) Yamaguti, 1954 accepted as Neoplagioporus zacconis (Yamaguti, 1934) Shimazu, 1990 (new combination reference)
Podocotyle aeglefini (Müller, 1776) Yamaguti, 1954 accepted as Podocotyle simplex (Rudolphi, 1809) Srivastava, 1966 (new combination reference)
Podocotyle producta (Stafford, 1904) Yamaguti, 1954 accepted as Podocotyle reflexa (Creplin, 1825) Odhner, 1905 (new combination reference)
Podocotyle virens (Sinitsin, 1931) Yamaguti, 1954 accepted as Allopodocotyle virens (Sinitsin, 1931) Pritchard, 1966 (new combination reference)
Proctoeces insolitus (Nicoll, 1915) Yamaguti, 1954 (new combination reference)
Protocladorchis burmanicus (Chatterji, 1938) Yamaguti, 1954 (new combination reference)
Pseudocreadium dampieriae (Yamaguti, 1942) Yamaguti, 1954 accepted as Hypocreadium dampieriae Yamaguti, 1942 (new combination reference)
Pseudohaplorchis Yamaguti, 1954 accepted as Tubanguia Srivastava, 1935 (original description)
Pseudohaplorchis anguillarum (Tubangui, 1933) Yamaguti, 1954 accepted as Tubanguia anguillarum (Tubangui, 1933) Yamaguti, 1958 (new combination reference)
Pseudohurleytrema Yamaguti, 1954 (original description)
Pseudohurleytrema eucinostomi (Manter, 1942) Yamaguti, 1954 (new combination reference)
Pseudosellacotyla Yamaguti, 1954 (original description)
Pseudosellacotyla lutzi (Teixeira de Freitas, 1941) Yamaguti, 1954 (new combination reference)
Stephanostomum edentulum (Linton, 1910) Yamaguti, 1954 accepted as Stephanostomum casum (Linton, 1910) McFarlane, 1936 (new combination reference)
Stephanostomum gracile (Vigueras, 1942) Yamaguti, 1954 (new combination reference)
Stephanostomum nipponicum Yamaguti, 1954 (original description)
Stephanostomum pacificum (Yamaguti, 1951) Yamaguti, 1954 (new combination reference)
Steringotrema ovacutum (Lebour, 1908) Yamaguti, 1954 (new combination reference)
Steringotrema quinquelobatum (Layman, 1930) Yamaguti, 1954 accepted as Stenakron quinquelobatum (Layman, 1930) Mamaev, Parukhin & Baeva, 1963 accepted as Stenakron vetustum Stafford, 1904 (new combination reference)
Tergestia Stossich, 1899 (subsequent type designation)

Japanese part of the Inland Sea for Stephanostomum nipponicum Yamaguti, 1954