Paulownia (Paulownia aulownia) is an economically important tree, which is used in the manufacture of paper and furniture industry. Moreover, it considered a medicinal plant used for treating a diversity of diseases. Buds were cultured on Murashige and Skoog (MS) solid medium supplemented with benzyl amino purine (BAP) and kinetin (KIN). The resulting plantlets were cultured on MS medium containing different sodium chloride (NaCl) concentrations (50, 100 and 150 mM). The survival percentage and mean shoot length of plantlets were calculated after eight weeks. The results revealed that the survival percentage and mean shoot length were decreasing with increasing NaCl concentration. In order to provide a reference for investigating the mechanism of salinity resistance, variations of anatomy and chloroplast ultrastructure in the leaves of unstressed and stressed plantlets (50 and 150 mM NaCl) after 16 days from culture were examined under photonic and electron microscopy. The results showed that salinity treatments induced variations in leaf mesophyll, changes in vascular bundle, deformed trichomes, and appearance of starch granules in chloroplasts. The diversity in phenotypic and ultrastructure of leaves considered as genetic markers of paulownia plantlets against salinity.