A new species of Marginella Lamarck, 1799 is described from the Early Pleistocene of the Messina Strait area, M. seguenzai n. sp. The remarkable variability in shell size and shape required a preliminary morphometric analysis, which provided evidence of a single species. This is the last known representative of the genus Marginella in the Mediterranean, today highly diverse in the tropical and subtropical shallow waters of West Africa, up to about 28°N. The genus Marginella was thought to have disappeared from the Mediterranean and the adjacent Atlantic after the Early Pliocene, due to early cooling phases. Anyway, Marginella seguenzai n. sp. was a deep water species, and its extinction was most probably due to the loss of psychrosphere, in the Early Pleistocene, rather than to climatic deterioration. The remarkable closeness between the new species and a deep water living species, endemic to three seamounts in the NE Atlantic, suggests a common origin for both species. High productivity seems to have been a key factor in the Mediterranean distribution of Marginella, either in shallow and deep waters.