Aim: In this study, the effects of Ni and Zn to leaf anatomy, some flavonoids and nitrotoxin of Coronilla varia were investigated.Material and Methods: 40 days aged grown Coronilla varia L. plants in equal growth condition were treated with different concentration of ZnCl2 (0, 7.5, 15, 22.5 and 30 mM) and NiCl2 (0, 2.5, 5, 7.5 and 10 mM) for 24 and 72 hours in hydroponic culture and the effects of imposing heavy metals on Leaf anatomy, some flavonoids of control and treated plants examined and compared using 2-DPC (Two Dimensional Paper Chromatography) and TLC (Thin Layer Chromatography) methods. Nitrotoxin measured using spectrophotometer too. All of Data compared together.Results: Results showed anatomical changes in polluted plants responses to Zn and Ni. In general results showed a wide changes in leaf flavonoids profile with increases number of total flavonoids at Zn and Ni stress. However, Nitrotoxin increased significantly when Zn and Ni increased.Conclusion: Probably, C. varia L. can tolerate against heavy metals stress of Zn and Ni with changes of flavonoids content and nitrotoxin.