Foraminifera and calcareous nannofossils from washed drill-cuttings of three wells in the Chilean sector of the Magallanes Basin were studied. This contribution aims to identify, characterize and illustrate microfossil assemblages throughout the Cenozoic sedimentary record to integrate foraminiferal and nannofossil data, and improve further biostratigraphic studies in the basin. The analyzed Paleogene and Neogene successions in these three wells correspond to five discrete foraminiferal and nannofossil assemblages, which were recognized and are described here: the early-middle Paleocene assemblage is mainly characterized by agglutinated foraminifera and few nannofossil species like Chiasmolithus danicus and Prinsius tenuiculus; the early Eocene assemblage is represented by low diversity and oceanic species, consisting of planktic foraminifera like Subbotina triloculinoides, radiolarians and calcareous nannofossils including Chiasmolithus bidens and Toweius pertusus; the middle-late Eocene assemblage is the most diverse of all those distinguished in this study, as it contains a rich microfauna of benthic and planktic foraminifera including the species Elphidium saginatum, Virgulinella severini, and Globigerinatheka index, as well as numerous nannofossils like Chiasmolithus solitus, C. oamaruensis and Reticulofenestra reticulata; the early Oligocene marks the turnover to a reduced assemblage including Subbotina angiporoides and Chiasmolithus altus; and ultimately, the late Oligocene-early Miocene assemblage, characterized by a low species richness of mainly nonionid foraminifera and reticulofenestrid nannofossils. A detailed systematic list of both foraminiferal and nannofossil species is presented, intended to serve as a catalogue that will help to identify the different Cenozoic assemblages of the basin in future studies.