The response of coccolithophore export production to non-El Niño and El Niño conditions was monitored during a two year period (26 March 1996-3 April 1998) in the centre of the Santa Barbara Basin (34°14′ N; 120°02′ W), California borderland. During the 1997-1998 El Niño the seasonal cycle of the surface water conditions was altered by the presence of a relatively warm, low-nutrient and low-salinity water mass. Throughout the studied period, the total mass flux is dominated by lithogenic components with terrigenous input being highest during El Niño period. Although the annual biogenic sediment fluxes were largely dominated by silica, with diatoms as the major contributor to the opal flux, the coccolith flux was high during the entire studied period. During winter 1998 carbonate fluxes were unusually high for this time of the year. Moreover, a strong positive correlation between organic carbon and opal flux indicates that siliceous phytoplankton production is the most important factor controlling organic carbon flux in the Santa Barbara Basin. A positive correlation between carbonate and organic carbon fluxes existed indeed during the final phase of El Niño, when the correlation between organic carbon and opal fluxes is poor. The sinking coccolithophore assemblage was dominated by Emiliania huxleyi, followed by Florisphaera profunda, Umbilicosphaera sibogae, Gephyrocapsa oceanica, Helicosphaera carteri, Gephyrocapsa muellerae and Calcidiscus leptoporus. The intensification of El Niño 1997-1998 conditions altered the typical hydrographic structure of the Santa Barbara Basin weakening the spring upwelling as reflected by reduced diatom fluxes. In contrast, the coccolith flux was relatively high during El Niño, particularly for the tropical species G. oceanica, that showed a pronounced increase in its flux when the spring upwelling was reduced under El Niño conditions. In addition, we have found that this species has a strong correlation with nitrite, phosphate and iron availability in surface water. © 2005 Elsevier B.V. All rights reserved.