Oxygen isotope data from planktonic foraminifera for the warm Eocene epoch suggest that tropical sea-surface temperatures (SSTs) may have been cooler than at present. Such data have stimulated various explanations involving, e.g., major changes in ocean heat transport. However, the planktonic data disagree with terrestrial climate proxies, which suggest significantly warmer low-latitude temperatures. We examined this discrepancy by analyzing seasonal oxygen isotope variations in shallow-marine mollusks from the Mississippi Embayment. Results indicate that mean annual SSTs decreased from 26–27 °C in the early Eocene to 22–23 °C in the Oligocene, agreeing well with temperatures inferred from terrestrial climate proxies. These cooling trends, with more significant winter cooling (5 °C) than summer cooling (3 °C), are consistent with the predicted consequences of decreasing atmospheric CO2 concentration through the Paleogene, suggesting that atmospheric CO2 change was a major controlling factor for Paleogene climate change. That winter SST estimates from the mollusks agree well with the foraminiferal SST estimates suggests that planktonic foraminiferal growth in low latitudes occurred mainly during the cooler winter months throughout the Eocene. We hypothesize that the unusual hydrography of Eocene oceans shifted foraminiferal productivity primarily to winter, biasing foraminiferal SST estimates of mean annual SSTs.