Background: Heart failure with preserved ejection fraction (HFpEF) is associated with endothelial dysfunction, but the molecular mechanisms still remain unclear. Whether exercise training (ET) along with which optimal modality can improve endothelial function is controversial. The present study used a hypertensive, diabetic-driven HFpEF animal model (ZSF1 rats) to determine whether different training modalities (moderate-continuous (MCT) and high-intensity interval training (HIIT)) could reverse endothelial dysfunction and to understand the underlying molecular mechanisms. Methods and results: The development of HFpEF in ZSF1 obese animals was confirmed by echocardiography and hemodynamic measurements. Thereafter, animals were randomized into following groups: 1) sedentary, 2) 8 weeks of MCT, 3) 8 weeks of HIIT. ZSF1 lean animals served as control. In vitro measurement of endothelial function in aortic rings revealed significantly impaired endothelial-dependent and -independent vasodilation in HFpEF, which was reversed by MCT and HIIT. At the molecular level, the development of endothelial dysfunction was associated with a reduced expression / activation of endothelial nitric oxide synthase (eNOS), an increase in NADPH and activation of c-Jun N-terminal protein kinase (JNK), a reduced collagen I/III ratio and a reduced lining of the vessel wall by endothelial cells. ET primarily decreased NADPH oxidase expression, and JNK activation, elevated collagen I/III ratio while further improving aortic endothelial cell coverage. Conclusions: The present study provides evidence that endothelial dysfunction occurs in experimental HFpEF and that ET, independent of the studied training modality, reverses endothelial dysfunction and specific molecular alterations. ET may therefore provide an important therapeutic intervention for HFpEF patients.