A better understanding of the factors responsible for the variability in Indian summer monsoon rainfall (ISMR) is important in the present day climate because it is vulnerable to climate change. Here, we report the relationship between the Atlantic and Pacific sea surface temperature (SST) anomalies with ISMR. We developed a new ISMR index based on the high correlation of the SST anomaly over the oceanic regions during March–April, prior to the southwest monsoon season. The study was performed by utilizing rainfall data from the India Meteorological Department and SST anomaly derived from monthly extended reconstruction sea surface temperature data. We found that the relationship of the SST anomaly in the southwest Pacific region during the March–April period with the following ISMR is persistent in the 31-year sliding window correlation analysis. SST anomaly in the Equatorial Atlantic during the March–April period is related almost in a similar manner to the following ISMR. However, persistence of the significance level is fluctuating. This indicates that the ISMR and the SST anomalies have varying relationships. To find out the fluctuation in the relationship between ISMR and the SSTs, we subjected the parameters to harmonic analysis. We noticed that the SST anomalies have similar kind of variability in the multidecadal (32 year), decadal (10.5) and interdecadal (5.6) periodicities in both Atlantic and southwest Pacific regions. The harmonics of SST and ISMR in the multidecadal time scale is out of phase and that for decadal and interdecadal time scales are in phase.