An attempt has been made to differentiate percentage contribution of coherent structures (CS) in the turbulent fluxes of heat and momentum during thunderstorm days (TD) and non-thunderstorm days (NTD) at two tropical sites. Pre-monsoon months (Marcha to May) fast response data (10 Hz) of wind and temperature at Kharagpur (22°30′N, 87°20′E) for years 2007, 2009, and 2010, and at Ranchi (23°25′N, 85°26′E) for years 2008–2010 have been used. The contributions were calculated after decomposing the time series using wavelet technique by two methods: (1) the method of quadrant analysis for each scale, and (2) the method of zero-crossing. Contributions of CS in momentum flux are higher in TD than NTD, whereas for heat flux CS contribution is higher for NTD to that of TD at both sites; however, values are different at both sites and by each method as well. Significant percentages of contributions of CS to the total flux are noticed at both the sites.