First and last occurrences of 389 diatom species from the first global Cenozoic record are used to reconstruct the position of major oceanographic boundaries. First appearances and extinctions group in three latitudinal bands: middle to high northern latitudes, equatorial region, and high southern latitudes. Sparse Paleogene occurrences were limited to southern high latitudes along the equivalent of the modern Antarctic polar front. Its late middle Eocene to middle Miocene position varied within 10°, and within a 20° band from middle Miocene to present, suggesting an association with global cooling. First and last occurrence events appear in the two remaining latitudinal regions during the Eocene and increase in a stepwise fashion, mimicking significant cooling events. At about 16 Ma, first and last appearances shift from the North Atlantic to the North Pacific. Low-latitude data suggest low surface water productivity prior to 40 Ma, while increased abundance from the middle Miocene correlates with expansion of the east Antarctic Ice Sheet.