High-quality ocean color data (chlorophyll) provided by the Sea-viewing Wide Field of view Sensor (SeaWiFS) satellite were analyzed for the first complete year of coverage (October 1997 to September 1998) in the tropical Indo-Pacific basin. This period coincides with the peak of one of the strongest El Niño events during December 1997 and the La Niña of 1998 that appeared dramatically in less than a month as a sea surface temperature (SST) change of over 6°C in the central equatorial Pacific during June 1998. The tropical Indian Ocean also underwent a highly anomalous series of events with negative SST anomalies (SSTA) of over 3°C in the eastern equatorial and coastal regions during October-December 1997 and warm SSTA in the west that peaked at over 2°C during February 1998. The ocean color variability is interpreted using other satellite data such as sea level from TOPEX/Poseidon and also in terms of the dynamics and thermodynamics of the region from simulations with an ocean general circulation model. The El Niño-related reductions in equatorial production and the off-equatorial increase in biological activity, and their basin scale evolution is clearly seen for the first time. Persistent northerly wind anomalies resulted in a northward shift of the equatorial divergence and the upwelling Kelvin wave which signalled the end of the 1997–1998 El Niño. The anomalous surface chlorophyll associated with this Kelvin wave was also clearly shifted north of the equator by nearly 300 km and appeared more than a month before the negative sea level anomalies seen by TOPEX/Poseidon. On the equator near 165°E, the disappearance of the barrier layer appeared to coincide with a localized bloom that occurred in response to the easterly wind bursts over the western Pacific that lasted from December 1997 through the boreal summer. The ecosystem response to the cold La Niña conditions is clearly seen as elevated chlorophyll during the boreal summer of 1998 in the equatorial Pacific cold tongue region. In the Indian Ocean, an anomalous phytoplankton bloom was observed by SeaWiFS during October-December 1997 coincident with the anomalous upwelling in the eastern equatorial region and off the coast of Sumatra. A stronger than normal northeast monsoon is seen as higher than climatological values of surface chlorophyll. The open ocean Ekman pumping and the shoaling of the thermocline near 60°E and 10°S and the eastward extension of mixed layer entrainment in the same latitude band is seen as a region of higher biological activity during the boreal summer.