We analysed the variability of sea surface temperature (SST) and chlorophyll-a concentration (Chl-a) in the eastern Indian Ocean (EIO). We used monthly mean Chl-a and SST data with a 4-km spatial resolution derived from Level-3 Aqua Moderate-resolution Imaging Spectroradiometer (MODIS) distributed by the Asia-Pacific Data-Research Center (APDRC) for the period 2002–2017. Wavelet analysis shows the annual and interannual variability of SST and Chl-a concentration in the EIO. The annual variability of SST and Chl-a is influenced by monsoon systems. During a southeast monsoon, SST falls while Chl-a increases due to upwelling. The annual variability of SST and Chl-a is also influenced by the Indian Ocean Dipole (IOD). During positive phases of the IOD (2006, 2012 and 2015), there was more intense upwelling in the EIO caused by the negative anomaly of SST and the positive anomaly of Chl-a concentration.