From flora of North West of Iran, four contrasting species in term of frequency and coverage on heavy metal rich soils were selected to study physiological mechanisms for different tolerance of Zn and Cu toxicity in a hydroponic culture experiment. For study of Zn toxicity, Dactylis glomerata and Secale monatum and for Cu, Cichorium intybus and Astragalus echinops were selected. A clear difference was observed between S. monatum and D. glomerata for tolerance to Zn toxicity and between C. intybus and A. echinops for Cu toxicity. Higher sensitivity to Zn and Cu toxicity in D. glomerata and C. intybus was associated with higher Zn and Cu accumulation in root and shoot. In order to determine the possible role of chelating/detoxifying molecules, changes in the content of amino and organic acids in response to metal treatment were studied. A relative high citrate and malate content in D. glomerata in comparison with S. monatum, was not the reason of higher Zn tolerance. In contrast, endogenous malate content in A. echinops was accompanied by higher Cu tolerance in this species. Cysteine was the only possible chelating/detoxifying molecule for Cu, but not for Zn. Our results showed that a high Cu tolerance in A. echinops was associated with higher endogenous and inducible cysteine content of shoot. Activity of peroxidase decreased under Cu toxicity, interestingly, this reduction was much higher in C. intybus (susceptible) when compared with A. echinops (tolerant). Because of possible role of lignin in establishing an apoplasmic transport barrier, higher uptake and transport of Cu into shoot in C. intybus could be due to the result of stronger inhibition of guiacol peroxisdase i.e. inhibition of lignin formation, in this species under Cu toxicity.