Benthic foraminifera δ18O increased by 5.4 ‰ through the Cenozoic Era, the past 65 million years of Earth's history. This increase is attributed to growth of global ice sheets and global ocean cooling. On the other hand, δ18O measurements of planktonic foraminifera do not exhibit significant change. These measurements initially were interpreted to suggest cool tropical and subtropical temperatures and introduced the concept of the “cool tropics paradox”, in which global bottomwater temperatures were significantly warmer but tropical surface temperatures were not during the early Cenozoic. This lack of change in δ18O of planktonic foraminifera was explained by secondary postburial alteration of the primary planktonic isotope signal.We provide an alternative record of sea surface water characteristics of Cenozoic Era by measuring δ18O of siliceous microfossils. This scarce phase of marine silica, unaltered biogenic opal-A, composed of diatoms, radiolaria and sponge spicules, was separated and purified from deep-sea Cenozoic sediments. We measured δ18O of siliceous microfossils from a set of drilled cores: DSDP 278 from the South Pacific, DSDP 513 from the South Atlantic, and ODP 1050–1053 and DSDP 391 from the subtropical North Atlantic. The purity of the biogenic opal and its mineralogical phase was assessed with SEM, SEM/EDS, XPS, and XRD.The δ18O of biogenic opal-A fluctuates around an average value of 43.0 ‰ through the Cenozoic Era, comparable to the Southern Ocean average of 43.2 ‰ of diatoms and radiolaria from the last 30,000 years which represent the last glacial and interglacial period and suggesting cold surface temperatures of 2–7 °C, both in the subtropical and polar latitudes. Taking into consideration changes in δ18O associated with bottomwater interaction with the lower crust and changes in sea level associated with waxing and waning of ice sheets, we conclude lack of or minimal change in the surface water temperature through the Cenozoic Era. This revives the original idea of the “cool tropics” paradox with a carbonate independent δ18O record and without issues associated with diagenesis of benthic and planktonic foraminifera.