The present study was intended to reveal the differential isoesterase expression in leaves and roots of Vigna unguiculata L. in response to saline stress. Influence of NaCl (0, 3, 5, 7 and10 %) on seedlings of Vigna unguiculata L. was analyzed. The seedlings were grown in the centre for a period of 30 days. The randomly collected whole plants were used as a source for isoesterase isolation. The seedlings showed the maximum tolerance up to 10% of NaCl. The Poly acrylamide gel electrophoresis was performed by Anbalagan method. The staining and fixation of the enzyme was performed by the Sadasivam and Manickam method. Seedlings treated with various concentrations of NaCl showed different banding profile based on the concentration (0-10%) and duration (5-30 days) of salt treatment as follows: 32 bands with five active regions, 56 bands with eight active regions, 102 bands with eight active regions, 47 bands with seven active regions, 64 bands with nine active regions and 84 bands with nine active regions on 5th, 10th, 15th, 20th, 25th and 30th day respectively. The changing pattern of isozymes during development may be interpreted as evidence for differential timing of gene expression correlated with the physiological stress. The results of the present study concluded that the isoesterase patterns could serve as a useful biochemical marker of salinity.