A biozonation based on molluscs is proposed for Miocene deposits of western Amazonia (Peru, Colombia and Brazil), commonly referred to as the Pebas Formation. The new zonation refines existing pollen zonations and provides a key for the quick assessment of the stratigraphic position of Neogene deposits in the field. The regional distribution of twelve mollusc zones reveals a structuring of geological units around the broad Iquitos-Araracuara anteclise. The structure of the subsurface appears to have been a major factor in the determination of present-day second and lower order river courses in the study area. Based on this work a biostratigraphic framework for Miocene deposits of western Amazonia, including fossiliferous deposits from adjacent basins (Putumayo, Llanos and Magdalena basins in Colombia), is proposed.