Phytoplankton are crucial to marine ecosystems and the global carbon cycle. This study investigates the characteristics and causes of the interannual variation of the surface chlorophyll a (chl a) in the southern tropical Indian Ocean (STIO). We find that in addition to the Seychelles-Chagos thermocline ridge (SCTR) upwelling zone in the southwestern basin, large interannual variability also shows up in the southeastern tropical Indian Ocean (SETIO; 6°–18°S, 70°–92°E). The SCTR shows two dominant periods of four years and two years, whereas the SETIO shows a dominant period of six years and a weaker period of three years. Surface wind forcing anomalies within the STIO, but not the Indonesian throughflow, cause the interannual chl a anomaly. In the SETIO region, the thermocline dynamics control the chl a variation via a combination of equal contributions from local Ekman pumping and remote Rossby waves generated by the wind stress curl from the east. In the SCTR region, the thermocline dynamics explain only about 67% of the chl a variation, with a larger contribution from the remotely generated Rossby waves than local Ekman pumping. The circulation in the western basin also contributes to the chl a variation by transporting western equatorial chl a to this region during the boreal summer-fall. Both the Indian Ocean Dipole and the El Niño–Southern Oscillation act to modulate the chl a variation in the STIO. They make comparable contributions in the SETIO, while the Indian Ocean Dipole plays a more important role in the SCTR.