TEX86H- and UK37′-derived paleotemperatures, and isoprenoid glycerol dialkyl glycerol tetraether (GDGT), and alkenone concentrations were examined for ODP Site 1239 in the eastern equatorial Pacific (EEP) for the last 430 kyr. We propose that the difference between TEX86H- and UK37′-derived temperatures (∆T) and the abundance ratio of GDGTs to alkenones (GDGT/alkenone ratio) are potential upwelling indices which show consistent results with other upwelling indices. The ∆T and GDGT/alkenone ratio were maximal during the last five deglaciations, suggesting intensified upwelling. The intensification of upwelling in the EEP coincided with those at the Peru margin and in the Southern Ocean. This coincidence suggests that the reorganization of the Southern Hemisphere atmospheric circulation induced the intensification of the subtropical high-pressure cell, causing stronger southeast trade winds along the west coast of South America and the southern westerlies over the Southern Ocean, enhancing upwelling in both regions.