Pulmonary hypertension (PH) is characterized by increased pulmonary vascular remodeling, resistance, and pressures. Reactive oxygen species (ROS) contribute to PH-associated vascular dysfunction. NADPH oxidases (Nox) and mitochondria are major sources of superoxide (O₂^•−) and hydrogen peroxide (H₂O₂) in pulmonary vascular cells. Hypoxia, a common stimulus of PH, increases Nox expression and mitochondrial ROS (mtROS) production. The interactions between these two sources of ROS generation continue to be defined. We hypothesized that mitochondria-derived O₂^•− (mtO₂^•−) and H₂O₂ (mtH₂O₂) increase Nox expression to promote PH pathogenesis and that mitochondria-targeted antioxidants can reduce mtROS, Nox expression, and hypoxia-induced PH. Exposure of human pulmonary artery endothelial cells to hypoxia for 72 h increased mtO₂^•− and mtH₂O_2. To assess the contribution of mtO₂^•− and mtH₂O₂ to hypoxia-induced PH, mice that overexpress superoxide dismutase 2 (Tg^hSOD2) or mitochondria-targeted catalase (MCAT) were exposed to normoxia (21% O₂) or hypoxia (10% O₂) for three weeks. Compared with hypoxic control mice, MCAT mice developed smaller hypoxia-induced increases in RVSP, α-SMA staining, extracellular H₂O₂ (Amplex Red), Nox2 and Nox4 (qRT-PCR and Western blot), or cyclinD1 and PCNA (Western blot). In contrast, Tg^hSOD2 mice experienced exacerbated responses to hypoxia. These studies demonstrate that hypoxia increases mtO₂^•− and mtH₂O₂. Targeting mtH₂O₂ attenuates PH pathogenesis, whereas targeting mtO₂^•− exacerbates PH. These differences in PH pathogenesis were mirrored by RVSP, vessel muscularization, levels of Nox2 and Nox4, proliferation, and H₂O₂ release. These studies suggest that targeted reductions in mtH₂O₂ generation may be particularly effective in preventing hypoxia-induced PH.