Background and Objective: The breeding and selection of high-quality rice cultivars that have tolerant traits with salinity are involved in adapting to climate changes. Marker assisted selection (MAS) played a vital role in accurate and reliable screening methods. By applying SSR markers, the present study aimed to characterize the salt tolerance, aroma and amylose content of the BC3F6 generation, which is the hybrid between Jasmine 85 and Pokkali cultivars. Materials and Methods: The BC3F6 generation of the backcrossing hybrid from Jasmine 85 and Pokkali cultivars was evaluated with salt tolerance, aroma and amylose content. The SSR markers were employed to determine the relation to morphological characteristics. GelAnalyzer software was employed to determine the band sizes of each primer. Results: Based on the RM206 and RM201 markers, seven rice lines (P6, P7, P8, P9, P10, P11 and P12) carried salt-tolerant genes by specific band patterns. In terms of aromatic traits, all twelve rice lines contain 2 alleles of the recessive gene. Furthermore, there were 8 rice lines (P1, P2, P3, P4, P5, P6, P7 and P8) containing high levels of amylose, indicated by a Waxy marker. Thus, our results illustrated that three rice lines namely P6, P7 and P8 can tolerate and grow in salt environments. Moreover, yield trait genotypes such as aroma and amylose were also detected in such lines. Conclusion: The selected lines were potential breeding materials and should be evaluated in rice field conditions.