Closure of the Central American seaway was a local tectonic event with potentially global biotic and environmental repercussions. We report geochronological (six U/Pb LA‐ICP‐MS zircon ages) and geochemical (19 XRF and ICP‐MS analyses) data from the Isthmus of Panama that allow definition of a distinctive succession of plateau sequences to subduction‐related protoarc to arc volcaniclastic rocks intruded by Late Cretaceous to middle Eocene intermediate plutonic rocks (67.6 ± 1.4 Ma to 41.1 ± 0.7 Ma). Paleomagnetic analyses (24 sites, 192 cores) in this same belt reveal large counterclockwise vertical‐axis rotations (70.9° ± 6.7°), and moderate clockwise rotations (between 40° ± 4.1° and 56.2° ± 11.1°) on either side of an east‐west trending fault at the apex of the Isthmus (Rio Gatun Fault), consistent with Isthmus curvature. An Oligocene‐Miocene arc crosscuts the older, deformed and segmented arc sequences, and shows no significant vertical‐axis rotation or deformation. There are three main stages of deformation: 1) left‐lateral, strike‐slip offset of the arc (∼100 km), and counterclockwise vertical‐axis rotation of western arc segments between 38 and 28 Ma; 2) clockwise rotation of central arc segments between 28 and 25 Ma; and 3) orocline tightening after 25 Ma. When this reconstruction is placed in a global plate tectonic framework, and published exhumation data is added, the Central American seaway disappears at 15 Ma, suggesting that by the time of northern hemisphere glaciation, deep‐water circulation had long been severed in Central America.

Integration of several geologic lines of evidence reveals the prevalence of a lowland trans-Andean portal communicating western Amazonia and the westernmost Andes from at least middle Miocene until Pliocene times. Volcanism and crustal shortening built up relief in the southernmost Central and Eastern Cordilleras of Colombia, closing this lowland gap. Independent lines of evidence consist first, of field mapping in the Tatacoa Desert with a coverage area of ∼381 km2, 1,165 km of geological contact traces, 164 structural data points, and 3D aerial digital mapping models. This map documents the beginning of southward propagation of the southernmost tip of the Eastern Cordillera’s west-verging, fold-and-thrust belt between ∼12.2 and 13.7 Ma. Second, a compilation of new and published detrital zircon geochronology in middle Miocene strata of the Tatacoa Desert shows three distinctive age populations: middle Miocene, middle Eocene, and Jurassic; the first two sourced west of the Central Cordillera, the latter in the Magdalena Valley. Similar populations with the three distinctive peaks have now been recovered in western Amazonian middle Miocene strata. These observations, along with published molecular and fossil fish data, suggest that by Serravallian times (∼13 Ma), the Northern Andes were separated from the Central Andes at ∼3°N by a fluvial system that flowed into the Amazon Basin through the Tatacoa Desert. This paleogeographic configuration would be similar to a Western Andean, or Marañon Portal. Late Miocene flattening of the subducting Nazca slab caused the eastward migration of the Miocene volcanic arc, so that starting at ∼4 Ma, large composite volcanoes were built up along the axis of today's Central Cordillera, closing this lowland Andean portal and altering the drainage patterns to resemble a modern configuration.