Marine sedimentary rocks of the lower Miocene Monte León Formation of southeastern Patagonia (Austral Basin), Argentina are important geological archives for better understanding regional tectonics, paleoenvironments, oceanography, and climate. In this paper, we describe assemblages of invertebrates, palynomorphs, foraminifera, ostracods and calcareous nannofossils in a stratigraphical and sedimentological framework, which suggest deposition during a transgressive-regressive cycle. From base to top, the lowermost outcropping deposits of the Punta Entrada Member represent an inner shelf environment, formed during a transgressive phase. The zone of maximum flooding is marked by a high diversity of protoperidiniaceans (heterotrophic) and offshore dinoflagellate cysts, an increase in the percentage and size of planktonic foraminifera, and a decrease in shallow water benthic foraminifera. Regressive deposits in the upper part of the Punta Entrada Member exhibit a progradational stratal stacking pattern and are characterized by an upward decrease in bioturbation and in the content of marine invertebrates; the dinoflagellate cyst assemblages point toward shallower and more restricted marine conditions than in underlying deposits. The cycle ends with the Monte Observación Member, which contains an impoverished and mostly reworked fauna of invertebrates. The presence of monospecific reefs of Crassostrea orbignyi, the decrease in dinoflagellate cysts and calcareous microfossils diversity, and the increase of continental palynomorphs suggest progressively shallower conditions and increasing influence of freshwater discharge. Although eustatic controls could have contributed to the sedimentary evolution of the Monte León Formation, the upward regressive trend is interpreted as the result of tectonism linked to the Andean orogeny, which led to the uplift, exhumation, and erosion of the highlands in the west. This is supported by the abundance of pyroclastic material, together with reworked specimens of Upper Cretaceous forams and Upper Cretaceous and middle Eocene dinoflagellate cysts in the upper part of the Punta Entrada Member and in the Monte Observación Member.