Aqueous dimethyl sulfide (DMS) concentrations and its sea-to-air fluxes were studied in upper layers (200 m) of the Indian Ocean, as a part of the Indian Ocean Experiment (INDOEX) that centered around the movement of the Intertropical Convergence Zone (ITCZ). Observations during the January–March period revealed significant interannual differences in water column DMS concentrations between 1998 and 1999. DMS concentrations were about five times higher in 1999 (range: 0–14.84 nM; average: 3.32 nM) than 1998 (range: 0.05–4.94 nM; average: 0.70 nM). Similar variation was found with respect to its precursor, dimethylsulfoniopropionate (averages of 3.31 nM in 1998 and 16.36 nM in 1999). DMS exhibited weak relationships with nitrate and chlorophyll but a relatively strong one with mixed layer depths. Our results suggest that physical forcing (wind speed and depth of mixed layer) along with the associated biological processes might have primarily controlled DMS in these waters. The column DMS appears to be a function of mixed layer depth whereas interannual variability in its concentrations might be attributable to changes in wind forcing and plankton composition, Sea-to-air fluxes were higher (seven times) because of higher DMS abundance and wind speeds in 1999 (average: 7.2 μM m−2 d−1) than 1998 (average: 1.0 μM m−2 d−1). Higher DMS fluxes coincided with reported higher aerosol optical depths over the Indian Ocean in 1999.