This paper deals with the evaluation of parameterization schemes in the WRF model for estimation of mixing height. Numerical experiments were performed using various combinations of parameterization schemes and the results were compared with the mixing height estimated using the radiosonde observations taken by the India Meteorological Department (IMD) at Mangalore site for selected days of the warm and cold season in the years 2004–2007. The results indicate that there is a large variation in the mixing heights estimated by the model using various combinations of parameterization schemes. It was seen that the physics option consisting of Mellor Yamada Janjic (Eta) as the PBL scheme, Monin Obukhov Janjic (Eta) as the surface layer scheme, and Noah land surface model performs reasonably well in reproducing the observed mixing height at this site for both the seasons as compared to the other combinations tested. This study also showed that the choice of the land surface model can have a significant impact on the simulation of mixing height by a prognostic model.