The Putumayo foreland basin (PFB) is an underexplored hydrocarbon-bearing basin located in southernmost Colombia. The PFB forms a 250 km long segment of the 7000 km long corridor of Late Cretaceous-Cenozoic foreland basins produced by eastward thrusting of the Andean mountain chain over Precambrian rocks of the South American craton. We have used approximately 4000 km of 2D seismic data tied to 28 exploratory wells to describe the basin-wide structure and stratigraphy. Based on seismic interpretation and comparison with published works from the southward continuation of the PFB into Peru and Ecuador, three main across strike, structural zones include (1) the 20 km wide, western structural zone closest to the Andean mountain front characterized by inversion of older, Jurassic half-grabens during the Late Miocene, (2) the 45 km wide, central structural zone characterized by moderately inverted Jurassic half-grabens, and (3) the 120 km wide, eastern structural zone (ESZ) characterized by the 40 km wide, north–south-trending Caquetá arch. The five mainly clastic tectonosequences of the PFB include (1) Lower Cretaceous pre-foreland basin deposits, (2) upper Cretaceous-Paleocene foreland basin deposits, (3) Eocene foreland basin deposits related to the early uplift of the eastern Cordillera, (4) Oligocene-Miocene underfilled, foreland basin deposits, and (5) Plio-Pleistocene overfilled, foreland basin deposits. We used 3D flexural modeling to identify the elastic thickness () of the lithosphere below the PFB, and to model the location of the sedimentary-related and tectonically related forebulges of Cretaceous to Oligocene age. Flexural analysis finds two pulses of rapid, foreland-related subsidence first during the Late Cretaceous-early Paleocene and later during the Oligocene-Miocene. Despite the present-day oblique thrusting of the mountain front, flexure of the PFB basement has produced a tectonic forebulge now located in ESZ and controls a basement high that forms the eastern updip limit for most hydrocarbons found in the PFB.