Maize (Zea mays) is one of graminae plants that widely spread for many purposes wheter in food industry, feed, or bioenergy. Those high utilization required an increment in production, but unfortunately the the demands not in accordance with the volume of production since conversion of agricultural area increase lately. Indonesia has many of shoreline that recognized as marginal land where the salinity is high as well. This research try to obtain tolerant variant from two local cultivars that planted in Madura Island. Manding and Talango varieties were used as an explant for callus induction stage in MS supplemented with 2,4 D. The result showed that 4 ppm of 2,4 D were the best concentration to induce the callus in both varieties. The induced callus were exposed to medium MS that contained NaCl (0, 2500, 5000, and 7500 ppm). In 7500 ppm of NaCl, Manding variety has 100% of surviving callus, while Talango variety only 66,7%. Furthermore, Manding variety showed a better performance in callus weight improvement with 170 mg, while Talango gave no improvement in callus weight. The result of RAPD analysis indicated that the genome characteristic was different between initial callus and surviving callus. Only five primers were presence polymorphism i.e OPA 13, OPB 07, OPC 02, OPK 20, and OPU 19 from ten in total primers. Manding elected as high tolerance variety in Salinity stress, thus it proposed to be developed furthermore.