The geological, geophysical and geochemical data pertaining the previously known as Choco Basin, was compiled and reinterpreted. Today, two distinc Cenozoic basins, the Atrato Basin and the San Juan Basin are identified, each with its own geological history. They are bounded by the Istmina- Condoto Structural High, in fact, a paleo-high which intermitently acts as sedimentary barrier, i.e. source area. In the San Juan Delta Basin up to 9 km (?) of mainly clastic sediments were deposited, most probably since Paleocene time. In the Atrato Fore Arc Basin a 10 km thickness of Cenozoic sediments were seismically recorded. Both basins are sufficiently structured, as to produce potential hydrocarbon traps, mainly post-Miocene in age. The tecto-sedimentary framework in the San Juan Basin is controlled by the Istmina-Condoto Fault System in the NW and the Garrapatas Fault System in the SE. In the Atrato Basin the occurrence of growth faults is an outstanding feature.