During the early Pliocene warm period ( approximately 4.6-4.2Ma) in the Eastern Equatorial Pacific upwelling region, sea surface temperatures were warm in comparison to modern conditions. Warm upwelling regions have global effects on the heat budget and atmospheric circulation, and are argued to have contributed to Pliocene warmth. Though warm upwelling regions could be explained by weak winds and/or a deep thermocline, the temporal and spatial evolution of the equatorial thermocline is poorly understood. Here we reconstruct temporal and spatial changes in subsurface temperature to monitor thermocline depth and show the thermocline was deeper during the early Pliocene warm period than it is today. We measured subsurface temperature records from Eastern Equatorial Pacific ODP transect Sites 848, 849, and 853 using Mg/Ca records from Globorotalia tumida, which has a depth habitat of approximately 50-100m. In the early Pliocene, subsurface temperatures were approximately 4-5 degrees C warmer than modern temperatures, indicating the thermocline was relatively deep. Subsurface temperatures steeply cooled approximately 2-3 degrees C from 4.8 to 4.0Ma and continued to cool an additional 2-3 degrees C from 4.0Ma to present. Compared to records from other regions, the data suggests the pronounced subsurface cooling between 4.8 and 4.0Ma was a regional signal related to restriction of the Isthmus of Panama, while continued cooling from 4.0Ma to present was likely related to global processes that changed global thermocline structure. Additionally, the spatial evolution of the equatorial thermocline along a N-S transect across ODP Sites 853, 849 and 848 suggests an intensification of the southeast trades from the Pliocene to present. Large-scale atmospheric and oceanographic circulation processes link high and low latitude climate through their influence on equatorial thermocline source water regions and consequently the equatorial thermocline. Through these low latitude/high latitude linkages, changes in the equatorial thermocline and thermocline source water played an important role in the transition from the warm Pliocene to the cold Pleistocene. Abstract Copyright (2012) Elsevier, B.V.