Paleogene planktonic foraminiferal communities diversified in surface ocean habitats by the end of the Danian (61.3 Ma). The specialized depth ecologies were related to the initiation of photosymbiosis as a trophic strategy within the last representatives of Praemurica inconstans. Our data confirm that Acarinina and Morozovella lived in the surface mixed layer, since they record lower delta (super 18) O and higher delta (super 13) C than contemporaneous Globanomalina and Subbotina. However, prior to 56.5 Ma, the data from the southeastern Indian Ocean (Ocean Drilling Program Hole 761B) show a clear separation in both oxygen and carbon isotopes between Morozovella and Acarinina, suggesting that the latter calcified slightly deeper in the photic zone than the former. The water column during the Paleocene appears to have been more stratified, in terms of plankton communities, than previously realized and the resulting creation of different depth habitats played an important role in plankton diversification. The surface waters over the subtropical Indian Ocean probably had a shallower mixed layer and a stronger thermal gradient than, for example, that of the mid-Pacific where the delta (super 18) O offsets between different species of planktonic foraminifera are less pronounced. The different genera of planktonic foraminifera established distinct surface-ocean, shallow thermocline, and deep thermocline depth habitats that remained occupied by related species groups throughout the Paleocene. The invasion of planktonic foraminifera into the oligotrophic gyres during the middle Paleocene led to a significant diversification that was fueled by photosymbiosis in the planktonic foraminifera.