Perturbations to phytoplankton biomass associated with the onset of the 1997--98 El Ni¿o event are described and explained using physical and bio-optical data from moorings in the central equatorial Pacific. The physical progression of El Ni¿o onset is depicted, from reversal of the trade winds in the western equatorial Pacific, through eastward propagation of equatorially trapped Kelvin waves and advection of waters from the nutrient-poor western equatorial warm pool. Fluctuations in chlorophyll and quantum yield of fluorescence are tightly coupled to thermocline variations. ¿ 1998 American Geophysical Union