Cotton is one of the most economically important crops. Screening and selection salt-tolerant cotton genotypes using DNA molecular markers not only introduces tolerant cultivars valuable for hybridization and breeding programs, but also identifies DNA regions implicated in the salinity tolerance mechanism. Screening and selection of cotton genotypes resistant to salinity stress and Verticillium wilt disease using DNA molecular markers not only introduces tolerant cultivars valuable for hybridization and breeding programs, but also identifies DNA regions implicated in the tolerance mechanism. The lowest Disease Severity Index was recorded in AP-317 (0.37) and Tashkent-2 (0.32) varieties. A total of 63 bands were generated based on 12 ISSR primers, 50 of which were polymorphic. The highest PIC value was recorded for UBC841 (0.466). AP-317 of Azerbaijan origin and Kirqizistan-174 of Kyrgyzstan origin were the most distant (0.358) genotypes and at the same time showed high resistance to Verticillium wilt. The obtained results showed that ISSR markers were an effective tool for determining genetic variation and identification of cotton cultivars.