A 290-m-thick middle Cretaceous black shale sequence in the upper Magdalena Valley, a present-day intramontane basin located between the Central and Eastern cordilleras of Colombia, was investigated with organic-geochemical and microscopic analyses. As a result of the investigation, we were able to (1) differentiate four organic facies types, (2) estimate their source rock potential, and (3) integrate these facies into a sequence stratigraphic framework. The four organic facies types were type C, BC, B, and D. Type C contains a distinct terrigenous organic matter component in lowstand or highstand deposits. Organic facies type BC is characterized by an increase and a better preservation of marine organic matter. BC belongs to the lower part of the transgressive systems tract. Sediments of organic facies type B have the highest amount of marine organic matter due to excellent preservation under anoxic conditions. The absence of bioturbation and the enrichment of trace metals are further implications for deposition under anoxic conditions. Facies type B is found in the upper part of the transgressive systems tract and contains the best petroleum source rock potential. Facies B occurrence coincides with sea level highstand and correlates especially with a maximum flooding in northern South America during the Turonian. Organic facies type D is also related to highstand deposits, but shows a high rate of reworking and degradation of organic matter.