Salinization, as a serious climate change phenomenon, continues to cause critical issues for soils and crops. Abundance of genetic diversity of plants could contribute in solving the impacts of salinity. However, the relations between physiological and molecular traits of plant species need deep investigation and interpretation. Pot experiments were conducted in the greenhouse to investigate the difference in behavior between two amaranth species when they were beforehand subjected to salinity-stress conditions, specifically on some specific physiological and molecular characteristics. After 45 days from transplanting, salt stress was induced using a 150 mM sodium chloride solution. Treatments were arranged in randomized complete block design using three replications. After 0, 2, 6, 10, and 24 h, samples were collected to evaluate physiological data as well as diversity of gene expression. The samples were immediately frozen in liquid nitrogen and stored in -80⁰ C ultralow temperature refrigerators. Findings revealed that the red amaranth species (Amaranthus cruentus) was more tolerant to saline stress than the green amaranth species (Amaranthus hypochondriacus). Result data revealed that malondialdehyde (MDA) content in the red amaranth increased after 2 h then decreased (after 6 and 10 h) before rising again after 24 h. In the green amaranth, MDA content initially decreased after 2 h before increasing and later decreasing in a zigzag pattern ending in an increase after 24 h. There was an initial steep rise in proline content of green amaranth after 2 h which continued to still rise moderately till 24 h. In the red amaranth the initial rise in proline continued after 2, 6 and 10 h before it stopped. Results also showed that red amaranth gave higher value of superoxide dismutase (SOD) activity as compared with green amaranth in all tested salinity exposure times. The investigation on the expression of four genes assessed through quantitative PCR indicated the efficiency of red amaranth in increasing the expression of SOS1, HKT1, NHX1, and DGR2 genes, which encode adaptation-related proteins under salinity stress. In summary, the current work demonstrated that red amaranth could be an efficient genetic resource in improving salt-tolerant genotypes belonging to Amaranthus genus.