The Late Miocene was a period of major paleogeographic, climatic and biotic changes for the Mediterranean due to the restriction of the marine gateway to the Atlantic, which culminated to the Messinian Salinity Crisis (MSC), and the ongoing global climatic cooling. The Late Miocene ecological crisis very likely affected biodiversity of bivalves living in the Mediterranean during that time. In this study, we investigate the consequences of the Messinian Salinity Crisis and its preconditioning phase for the evolution of functional diversity of the Mediterranean bivalve fauna. The biodiversity of bivalves is quantified for the Tortonian, the pre-evaporitic Messinian and the Zanclean of the Mediterranean using the functional richness index, by considering the following bivalve species traits: lifestyle, depth range, maximum adult size, trophic role and substrate affinity. The analysis is based on a recently compiled dataset containing the updated fossil record of the Mediterranean bivalves for this time interval. The traits of the species in this dataset is obtained from online open-access databases and the literature. Our results support a decrease in the functional diversity of bivalves in the Mediterranean from the Tortonian to the Early Messinian and a full recovery in the Early Pliocene.