Margaritiferidae is an ancient freshwater bivalve family originated in the Jurassic in East Asia. Here, we revise several nominal taxa of fossil freshwater pearl mussels that were recovered from the Upper Pliocene and Pleistocene deposits of the Dniester and Prut river valleys. Based on morphological and stratigraphic data, we found that these nominal taxa belong to the genus Pseudunio and are junior synonyms of P. flabellatiformis (Grigorowitch-Beresowski, 1915). The new synonymy is proposed as follows: Margaritifera (Pseudunio) moldavica Chepalyga, 1964 syn. nov., Margaritifera (Pseudunio) robusta robusta Chepalyga, 1964 syn. nov., Margaritifera (Pseudunio) robusta speensis Chepalyga, 1964 syn. nov., and Margaritifera (Pseudunio) robusta tirassica Chepalyga, 1964 syn. nov. All these fossil nominal taxa were described based on minor differences in the shell shape and size, hinge structure, and stratigraphic position. Finally, we suggest an updated phylogenetic scheme of the genus Pseudunio, which contains five valid species: P. marocanus (Pallary, 1918) [Eocene-Recent, Morocco], P. auricularius (Spengler, 1793) [Pliocene-Recent, Southern and Western Europe], P. homsensis (Lea, 1865) [Pliocene-Recent, Orontes and Nahr al-Kabir basins], P. flabellatiformis (Grigorowitch-Beresowski, 1915) comb. rev. [Pliocene-Late Pleistocene, paleo-Dniester and paleo-Danube basins, an extinct lineage related to P. auricularius and P. homsensis], and P. flabellatus (Goldfuss, 1837) comb. rev. [Miocene, paleo-Danube Basin, a stem lineage, MRCA of P. auricularius-P. homsensis clade].