In the Paleogene to earliest Neogene, foraminiferal and molluscan faunas from the Caribbean and Eastern Pacific were reported as quite similar. Four million years ago the tropical seaway that connected the two oceans closed completely, and today the two faunas are different in composition. We compare the benthic foraminiferal faunas of two formations from either side of the Central American isthmus that are from the same time interval, planktic foraminiferal Zone N17 (8.3–5.6 Ma), and the same general bathymetry, middle neritic.

The Rio Indio facies of the Chagres Formation, which crops out near the Caribbean entrance to the Panama Canal, is middle neritic. Benthic foraminiferal assemblages are dominantly Atlantic in affinity or cosmopolitan, and include few taxa that are or were primarily Pacific.

The Angostura Formation, NW coast of Ecuador, includes middle neritic and shallow outer neritic facies exposed along the Rio Santiago and Punta Verde, respectively. Unlike most of the Miocene neritic sediments of Panama and Colombia, these were well oxygenated and contained diverse faunas, allowing direct comparison with those of the Caribbean. The deeper assemblage of benthic foraminifera contains more endemic species (e.g., Epistominella sandiegoensis, Hanzawaia evansi) than does the shallower assemblage, but many of the species were still transisthmian in the Late Miocene.

The species distributions indicate a stage of developing endemism in Late Miocene, Eastern Pacific faunas. The deeper, outer neritic faunas of the Angostura Formation show greater divergence with the Caribbean than shallower, middle neritic faunas. Deeper faunas should have been affected first by the rise of the sill that severed the connection between tropical Atlantic and Eastern Pacific faunas.