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Arsenic (As) is a carcinogenic element present in the environment, hence, detrimental to biota. Rice due to highly expressed silicon pathways accumulates As more than other cereals crops. Moreover, this cereal is the major staple diet of billions of people. The current study was done to analyze the responses of two contrasting rice (Oryza sativa L.) genotypes [high As accumulating rice genotypes (HAARG) and low As accumulating rice genotypes (LAARG)] in terms of thiol and phytochelatins (PCs) synthesis, during arsenate (AsV) and arsenite (AsIII) exposure. AsV and AsIII moderated the thiolic pathway which was evident by different metabolite levels in two genotypes. The synthesis of PCs and consequently the formation of PC-As complexes under As stress was more in HAARG than in LAARG. It may be considered that the plants triggered synthesis, as well as, consumption pathway of thiols to counter As toxicity. However, elevated concentration of AsV and AsIII caused disturbances of this balance resulting in phytotoxicity in HAARG even after the accumulation of a higher level of PCs. In contrast, LAARG showed less up-regulation of PCs, however, it was adequate to combat relatively low As concentrations. The results indicate that if the synthesis of thiols and PCs are stimulated to an optimum level, it helps rice plants tolerate As toxicity effectively.