The geographical location of the Azores, midway between Europe and America, poses problems relative to their colonization and the biogeographic affinity of the biota presently living there. In the way of the Gulf Stream, originating off American shores, the Azorean biota, marine and terrestrial alike is predominantly European. To explain this distributional paradigm the present study investigates the Neogene fossil record of Santa Maria, Azores in order to establish the biogeographical relationships of the Pleistocene to Recent littoral molluscan fauna of this archipelago. The bulk of the Azorean malacofauna, both in the Pleistocene (71.3%) and in Recent times (75.6%) is biogeographically related with the eastern Atlantic, and that the Pleistocene (Eemian) fossil fauna is basically the same as the Recent fauna, with a few losses of tropical species and of shallow water bivalves associated to fine sand substrates.It is hypothesized that during Pleistocene glacial-interglacial cycles, short-duration events have occurred during which short-lived oceanic currents must have been established, especially during or shortly after glacial terminations. During these short-term events, the arrival of species to the Azores may have been increased and facilitated by temporary sea-surface currents that no longer exist now. Probable routes of dispersal to the archipelago of the Azores are also discussed, as well as the possible influence of the Pleistocene glaciations in the shallow water marine molluscs of these islands.