Salinity is one of the most important limitation factors in development of agricultural products. Cotton has a relative tolerance to salinity; however, salinity reduces its growth during germination and seedling stages. In this research, split-factorial design of time based on randomized complete block design with 3 replications was used. The real-time PCR results for, root, stem, and leaves of 14-day cotton seedlings of tolerant (Sepid) and sensitive (Thermus14) cotton cultivars with salinity levels from 0 to 16 ds. m-1 were analyzed at three time points, namely 0, 7 and 14 days after salinity stress. Selected genes for Real Time PCR reaction in current study were selected using Cytoscape 3. 3. 0 software. Results showed that the selected genes GhERF2, GhMPK2, GhCIPK6, GbRLK, GhNHX1, GhGST, GhTPS1 and Gh14-3-3 have positively responded to salinity stress and their expression in the root was higher than in stem and leaf. Moreover, the expression of tolerant genotype (Sepid) was higher than the sensitive cultivar (Thermus 14) one, however, a slight increase in sensitive genotypes was observed in a number of genes (GhERF2 and GhGST) 14 days after starting the stress treatment.