The 1997/1998 El Niño Southern Oscillation (ENSO) was detected through observation of satellite-derived ocean color data (expressed as chlorophyll a) in the Indonesian seas. In addition to ENSO, other forcings may influence chlorophyll a concentrations in the Indonesian seas, such as tides (Ffield and Gordon, 1996; Susanto et al., 2000), the Madden-Julian Oscillation (MJO) (Madden and Julian, 1994), Kelvin and Rossby waves (Arief and Murray, 1996; Sprintall et al., 2000), monsoons (Asanuma et al., 2003; Moore et al., 2003; Susanto et al., submitted), and the Indian Ocean Dipole (IOD) (Saji et al., 1999; Webster et al., 1999). Because of its longitudinal extent (90° to 141°E), the Indonesian seas contain a significant part of the tropical ocean productivity. The majority of the ocean’s productivity occurs within the tropics along the equatorial band of 10°N to 10°S (Longhurst, 1993). The Indonesian seas are also a center of biological diversity (Veron, 1995). They are one of the regions in the world that exhibits high variability in ocean color (Yoder and Kennelly, 2003). And, the Indonesian seas are the sites of important fisheries, such as off the Halmahera coast (western Pacific warm pool region; Lehodey et al., 1997) and in the upwelling region in the eastern tropical Indian Ocean along the southern coasts of Java and Sumatra.