A field experiment was conducted for two consecutive seasons to study the effect of different concentrations of sodium azide (SA) and sodium nitroprusside (SNP) on some nutritional and anti-nutritional components in quinoa grains (Chipaya and Q37) under saline stress conditions in Ras Sudr, South Sinai. The results showed that quinoa was an excellent source of vitamins, essential and non-essential amino acids, and minerals, as well as some other medicinal compounds that are beneficial to health. It was found that the treatment with SA at a concentration of 0.04% had a positive effect on the decrease in the content of anti-nutritional compounds (saponins), and this was associated with a clear increase in grain yield of the Chipaya genotype under saline stress conditions. The same genotype recorded the highest rate of water-soluble vitamins (B1, B2, B9, and B12) as well as essential and non-essential amino acids when treated with SNP at a concentration of 0.75 mg/L. On the other hand, the genotype Q37 gave high values of essential and non-essential amino acids when treated with SA at a concentration of 0.04%. As for the mineral content of quinoa grains, it was found that the Chipaya genotype gave the highest manganese content when it was treated with SNP at a concentration of 0.25 mg/L. The highest content of zinc was recorded when it was treated with SA at 0.03%. The study also showed that, the same genotype recorded the highest iron content when it was treated with SA at a concentration of 0.01%. The use of molecular markers (ISSR-PCR) is crucial to identifying variation in genotypes, especially parameters that may lead to a change in genotypes. The study showed that the least polymorphism was detected by Q37 under salinity stress conditions and chemical treatments. This study confirms that the chemicals used (especially SA at a concentration of 0.04% and SNP at 0.75 mg/L), had a clear positive effect on increasing the content of nutritional components and decreasing the content of anti-nutritional contents in quinoa grains, and they did not cause a change in the genetic composition. Continuing the study on these chemicals with higher concentrations is recommend to obtain genotypes with desirable characteristics in terms of production and chemical composition.