Nannofossil assemblages from core MD02-2510 provide a ~ 22 ka record of past oceanographic variability in Alfonso Basin (Gulf of California, east subtropical Pacific). In this area, environmental conditions depend on a monsoonal system heavily influenced by changes in the location of the ITCZ and nearby atmospheric pressure centers. To reconstruct nutricline depth and ENSO-like variability, two ecological indexes were calculated based on the relative abundance of the three dominant coccolith species. The late glacial period is characterized by intensified wind-driven upwelling, high primary productivity and La Niña-like conditions. An environmental shift occurs during the glacial–interglacial transition, El Niño-like conditions intensify, nutricline deepens and surface productivity declines. The late Holocene is characterized by a persistent increase in nutricline depth and dominance of El Niño-like conditions. The fluctuations in the composition of the coccolith assemblages can be related to orbital-scale fluctuations in the average position of the ITCZ. However, while the ENSO-like signal that overprints the record varies in response to orbital forcing, on suborbital time scales the relation between ENSO-like conditions and the average position of the ITCZ and the North Pacific High changes, suggesting that the development of persistent El Niño-like conditions is strongly dependent on the specific climatic background.