This paper reports the first fossil (Tertiary) occurrence of freshwater sponges of the genus Ephydatia in the southern hemisphere. The sponges appear in diatomite lacustrine sediments of Late Miocene Quillagua Formation (Chile, Atacama region). The investigated specimens represent a new species, Ephydatia chileana sp. nov., which is close to the Recent cosmopolitan E. fluviatilis. On the basis of sedimentological and diatom assemblage data, sponge-bearing diatomites have been interpreted as deposited in open offshore shallow lacustrine conditions with slightly alkaline waters. The sponges show malformations, similar to some diatoms and probably caused by high heavy metal concentrations in a lake water. These concentrations are related to hydrothermal activity, which favored the leaching of volcanic rocks that outcrop extensively in the catchment