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)
Dentalium edoensis Tokunaga, 1906 † accepted as Ditrupa gracillima Grube, 1878 (original description)
Lasaea striata Tokunaga, 1906 † accepted as Chavania striata (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 parva Tokunaga, 1906 † accepted as Inquisitor tokunagae H. J. Finlay, 1927 † (original description)
Rissoa septentrionalis Tokunaga, 1906 † accepted as Finella purpureoapicata Preston, 1905 (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 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]