Exchange of mass (water vapor), momentum, and energy between atmosphere andocean has profound influence on weather and climate. This exchange takes place at the air-sea interface, which is part of the marine atmospheric boundary layer. Various empirical relations are being used for estimating these fluxes in numericalweather and climate models but their accuracies are not sufficiently verified or tested over the Indian Ocean. The main difficulty is that vast areas of open oceans are not easily accessible. The marine environment is very corrosive and unattended long term and accurate measurements are extremely expensive. India has research ships that spend most of their time over the seas around India but that opportunity is yet to be exploited. To address this, an air-sea flux measurement system for operation on board research ships was planned. The system was tested on board Indian Research Vessels ORV SagarKanya during its cruise SK-296 in the Bay of Bengal (BoB) in July-August 2012, and NIO ship Sindhu Sadhana in June-July 2016. The complete set included instruments for measuring wind velocity, windspeed and direction, air and water temperature, humidity, pressure, all components of radiation and rainfall. In addition, ship motion was recorded at required sampling rate to correct for wind velocity. The set up facilitates the direct computation of sensible and latent heat fluxes using the eddy covariance method. In this thesis, design and installation of meteorological and ship motion sensors onboard research ships, data collection and quality control, computation of fluxes of heat, moisture and momentum using eddy covariance method and their comparison with those derived from bulk method are described. A set of sensors (hereafter, flux measuring system) were mounted on a retractable boom, ~7 m long forward of the bow to minimize the flow disturbance caused by the ship superstructures. The wind observed in the ship frame was corrected for ship motion contaminations. During the CTCZ cruise period true mean wind speed was over 10 m/s and true wind direction was South/South-Westerly. True windspeedis computed combiningdata from the anemometer a compass connected to AWS and a GPS. Turbulent fluxes were computed from motion-corrected time-series of high frequency velocity, water vapor, and air temperature data. Covariance latent heat flux, sensible heat flux, and wind stress were obtained by cross-correlating the motion-corrected vertical velocity with fast humidity fluctuations measured with anIR hygrometer, temperate fluctuation from sonic anemometer and motion-corrected horizontal windfluctuations from sonic anemometer, respectively. During the first attempt made in July-August 2012 as part of a cruise of CTCZ monsoonresearch program, observations were mainly taken in the North Bay of Bengal. The mean air-temperature and surface pressure were ~28 Deg C and ~998 hPa, respectively. Relative humidity was ~80%. Average wind speed varied in the range 4-12 m/s. The mean latent heat flux was 145 W/m2 , sensible heat flux was ~3 W/m2 and average sea-air temperature difference was ~ 0.7°C. The Bay of Bengal boundary layer experiment (BoBBLE) was conducted during June-July 2016 and the NIO research ship Sindhu Sadhana was deployed. The same suite of sensors installed during CTCZ were used during BoBBLE. During daytime, peaks of hourly net heat fluxes (Qnet ) were around 600 Wm-2(positive if into the sea), whereas, night time values were around -250 W m-2. Sea surface temperature was always >28°C and maximum air temperature exceeded 29°C. During the experimental period the mean Qnet was around -24 Wm-2 from both eddy covariance and conventional bulk methods, but there are significant differences on individual days.The new flux system gives fluxes which are superior to what was available before.