To investigate effects of Ziziphora clinopodioides Lam. flavonoids on ischemia-reperfusion injury of myocardial cells. After application of 6.25, 25, and 100 μg/mL Ziziphora clinopodioides Lam. flavonoids to H9C2 myocardial cells for 24H, they were treated for 4 hours with hydrogen peroxide to induce oxidative damage, whereas controls were cells without treatment and cells only incubated with hydrogen peroxide. Cell viability, lactate dehydrogenase release and mitochondrial membrane potential, intracellular Na+/K+-ATPase activity and ATP content, and reactive oxygen species formation were monitored. An ischemia-reperfusion injury rat model was established by left anterior descending coronary artery ligature in 48 Sprague-Dawley rats, which were divided into positive control with isosorbide mononitrate (10 mg/kg) injection (n=8), model (ischemia-reperfusion, n=8), sham-operated (n=8), and Ziziphora clinopodioides Lam. flavonoids low (75 mg/kg, n=8), medium (150 mg/kg, n=8), and high concentration (300 mg/kg, n=8) groups. Superoxide dismutase activity and malondialdehyde content in homogenized hearts were measured and ischemic and infarction areas were triphenyl tetrazolium chloride and H&E stained for pathological and morphological examinations. Ziziphora clinopodioides Lam. flavonoids preconditioning improved cell viability (P<0.01), intracellular Na/K ATPase activity (P<0.001), and intracellular ATP content (P<0.001) and maintained mitochondrial membrane potential (P<0.05) in hydrogen peroxide treated H9C2 cells as well as rescued superoxide dismutase activity (P<0.01), decreased the malondialdehyde content (P<0.001), and reduced myocardial damage in the ischemia-reperfusion rat model (P<0.001) compared to the controls. Ziziphora clinopodioides Lam. flavonoids may be an effective drug for protecting myocardial tissue from ischemia-reperfusion injury by reducing reactive oxygen species related damage.