Despite the rich geological and paleontological record of Colombia, the Putumayo region near Ecuador remains one of the least explored regions in the equatorial Neotropics, mainly due to its thick vegetation, deep rock weathering, soil formation, and ground cover, geographic remoteness, and inaccessibility of well-exposed outcrops. This has resulted in limited comparisons with neighboring basins and thus the generation of more comprehensive biostratigraphic correlations with western and northern South America, as well as other paleobiogeographic regions (e.g., Tethys, Western Interior Seaway). Here, we present 67 occurrences of uppermost Lower Cretaceous to lowermost Upper Cretaceous ammonoids and other macrofossils (e.g., bivalves, decapod crustaceans, osteichthyan fish remains, plant remains), as well as a δ13Corg chemostratigraphic curve derived from 105 samples from the middle Albian of the uppermost Caballos Formation and the upper Albian to lower Cenomanian lower Villeta Formation, collected in situ from a stratigraphic section exposed along the Mocoa–San Francisco Road, Putumayo, Colombia, here called the San Francisco section. The chemostratigraphic, carbon-isotope curve for the region shows a great similarity with the shape of the accepted curve for the late Albian Oceanic Anoxic Event 1d, which is characterized by a worldwide long positive δ13C excursion anomaly. The new biostratigraphic and isotopic data serve as a point of reference to compare the Putumayo Basin with neighboring basins (e.g., Marañon Basin in Perú, Oriente Basin in Ecuador, Upper Magdalena Valley Basin in Colombia), and thus the generation of more comprehensive upper Lower Cretaceous and lower Upper Cretaceous biostratigraphic and chemostratigraphic correlations for northwestern South America.