Arca kagoshimensis Tokunaga, 1906 accepted as Anadara kagoshimensis (Tokunaga, 1906) (original description)
Arca rectangularis Tokunaga, 1906 accepted as Arca boucardi Jousseaume, 1894 accepted as Tetrarca boucardi (Jousseaume, 1894) (original description)
Arca tenuis Tokunaga, 1906 accepted as Anadara broughtonii (Schrenck, 1867) (original description)
Astarte japonica Tokunaga, 1906 † (original description)
Cardita rotunda Tokunaga, 1906 † accepted as Cyclocardia rotunda (Tokunaga, 1906) (original description)
Cardium braunsi Tokunaga, 1906 † accepted as Clinocardium braunsi (Tokunaga, 1906) † (original description)
Cardium tokyoensis Tokunaga, 1906 † (original description)
Cerithium (Cerithiopsis) tabatensis Tokunaga, 1906 † accepted as Cerithiopsis tabatensis (Tokunaga, 1906) † (original description)
Cerithium nipporiensis Tokunaga, 1906 † (original description)
Cylichna acuta Tokunaga, 1906 † (original description)
Cylichna musashiensis Tokunaga, 1906 accepted as Eocylichna musashiensis (Tokunaga, 1906) (original description)
Cylichna obtusa Tokunaga, 1906 † (original description)
Dentalium edoensis Tokunaga, 1906 † accepted as Ditrupa gracillima Grube, 1878 (original description)
Eulima levis Tokunaga, 1906 † (original description)
Lasaea striata Tokunaga, 1906 accepted as Chavania striata (Tokunaga, 1906) (original description)
Lima hakodatensis Tokunaga, 1906 accepted as Limaria hakodatensis (Tokunaga, 1906) (original description)
Lutraria ovalis Tokunaga, 1906 accepted as Lutraria australis Reeve, 1854 (original description)
Mysia pacifica Tokunaga, 1906 † (original description)
Odostomia takinogawnsis Tokunaga, 1906 † (original description)
Ostrea irregularis Tokunaga, 1906 † (original description)
Pecten pulchellimus Tokunaga, 1906 † accepted as Volachlamys hirasei (Bavay, 1904) (original description)
Pecten tokyoensis Tokunaga, 1906 † accepted as Mizuhopecten tokyoensis (Tokunaga, 1906) † (original description)
Pleurotoma (Drillia) tabatensis Tokunaga, 1906 † accepted as Guraleus tabatensis (Tokunaga, 1906) † (original description)
Pleurotoma (Mangelia) parva Tokunaga, 1906 † accepted as Inquisitor tokunagae H. J. Finlay, 1927 † (original description)
Pleurotoma ojiensis Tokunaga, 1906 † accepted as Clavus ojiensis (Tokunaga, 1906) † (original description)
Pleurotoma parva Tokunaga, 1906 † accepted as Inquisitor tokunagae H. J. Finlay, 1927 † (original description)
Pleurotoma sagamiensis Tokunaga, 1906 † (original description)
Rissoa meridionalis Tokunaga, 1906 † (original description)
Rissoa septentrionalis Tokunaga, 1906 † accepted as Finella purpureoapicata Preston, 1905 (original description)
Rissoa subcylindrica Tokunaga, 1906 † (original description)
Tellina nipponica Tokunaga, 1906 accepted as Macoma nipponica (Tokunaga, 1906) (original description)
Tellina ojiensis Tokunaga, 1906 accepted as Pristipagia ojiensis (Tokunaga, 1906) (original description)
Tellina serricostata Tokunaga, 1906 accepted as Serratina jonasi (R. A. Philippi, 1847) (original description)
Trochus (Calliostoma) shinagawensis Tokunaga, 1906 accepted as Calliostoma shinagawense (Tokunaga, 1906) (original description)
Trochus (Minolia) angulatus Tokunaga, 1906 † accepted as Conotalopia ornata (G. B. Sowerby III, 1903) (original description)
Turbonilla paucicostulata Tokunaga, 1906 (original description)

Honshu for Pecten pulchellimus Tokunaga, 1906 † 
Japan for Cardita rotunda Tokunaga, 1906 † 
Japan for Dentalium edoensis Tokunaga, 1906 † 
Japan for Lasaea striata Tokunaga, 1906 

 Homonymy

 for Pseudarcopagia minuta Scarlato, 1965

This species would become a secondary homonym of Tellina minuta Lischke, 1872, if represented as Tellina [details]