The resistance of plants to drought stress is very complex due to the complex interactions between stress factors and the variety of physiological, biochemical and molecular responses affecting plant growth and development. Therefore, it is necessary to know the effects of drought stress on plants. To investigate the effect of drought stress on yield (shoot fresh weight), morphological, phenological and biochemical characteristics in native basil masses, a randomized complete block design with Three replications were carried out in two separate environments in the research greenhouse of the Gulf University of Agriculture and Natural Resources, 1996-1996. Experimental treatments included normal (normal irrigation), 50% (severe) drought and 20 native basil populations collected from different parts of the country. Combined analysis of variance of both environments showed that there was a significant difference among the populations for all traits. Interaction of genotype in environment was also significant for all traits. Twelve ISSR primers were used to study and evaluate the genetic diversity of 20 native basil populations. The 12 ISSR primers produced a total of 94 bands, 55 of which showed polymorphism. In this study, the average number of bands per primer was 7.83. The number of polymorphic bands ranged from 2 to 8 bands. The average number of polymorphic bands was estimated to be 55 for each primer. The most polymorphic information content (PIC) was related to primer number 4 (0.49). Also, primer number 2 had the highest marker index (MI) (2.25), effective polymorphism ratio (EMR) (5.818), and polymorphism percentage index of 73%. Cluster diagram obtained by NTsys software using UPGMA method and Jaccard similarity coefficient. Also, two-dimensional and three-dimensional graphs were plotted using Principal Coordinate Analysis (PCoA) and the results of grouping were compared with cluster analysis. The grouping of the two methods was highly consistent. The highest