The debate regarding a possible marine influence during the middle—late Miocene in the Loja, Malacatos-Vilcabamba and Catamayo-Gonzanamá Basins (southern Ecuador) continues. To shed light on this controversy, we present a detailed stratigraphic and micropaleontological (benthic foraminifers and ostracods) study of selected sections from these basins. The facies associations, together with the presence of several benthic foraminifer species from marginal marine and open-water environments and ostracod genera resistant to high salinity changes, verify a marine water influence and sporadic marginal marine conditions in this area during certain periods of the middle—late Miocene. Additionally, six new ostracod species are hereby described: Heterocypris ballentae, Cyprideis lojaensis, Cyprideis petersonae, Cyprideis pachamama, Cyprideis tumi and Cyprideis amaru.