Qualitative and quantitative analysis of Middle/Late Miocene to Early Pleistocene marine ostracode assemblages from the South Aegean island arc showed some major fluctuations in species diversity and density. These fluctuations are related to regional changes of environmental conditions. In general the diversity and density were increasing during the Tortonian. A significant decrease coincides with the Messinian “salinity crisis”. The Pliocene and Early Pleistocene fauna is characterized by a very high diversity and density. A second period of decrease is found during the Late Pliocene. Discrete periods of phylogenetic radiation (cladogenesis), extinction and immigration are distinguished. Plate-tectonic movements related to the convergence of Africa and Europe during the Late Miocene and to Late Pliocene deformations in the Hellenic subduction zone were largely determining the faunal changes.