A pot experiment was conducted using three moderately resistant (PK1024, PK1029 and Ankur) and two susceptible genotypes (JS 335 and DSb1) of soybean to know the histological and morpho-physiological factors of resistance to leaf rust caused by Phakopsora pachyrhizi Syd. The resistant genotypes had thicker leaf lamina, epidermis and more number of epidermal cells per millimeter. Morpho-physiological studies indicated more number of stomata in susceptible genotypes than resistant ones. The lower surface of the leaves had more stomatal number than upper surface. Stomatal length, breadth and aperture length were more among resistant genotypes than susceptible genotypes. The wax content was higher in Ankur (0.45 µg mm-2).