The goal of the present study was to investigate the molecular mechanisms that underlie heart and skeletal muscle damage in male Wistar rats weighing 200–250 g in response to a 3-h exposure to 180 mm Hg (5% O2) in the model of severe hypobaric hypoxia. It has been demonstrated that the level of the cardiac biomarker troponin I in the blood plasma of rats exposed to severe hypobaric hypoxia for 3 h increased significantly compared to the control group, indicating myocardial injury. At the same time, the administration of the HIF-1α transcription factor inhibitor did not affect the plasma level of troponin I. In contrast, the release of the non-specific biomarker myoglobin into the bloodstream did not increase in response to hypoxia compared to the control animals. In addition, 24 h after the exposure to severe hypobaric hypoxia the serum myoglobin level was significantly lower in animals administered with the HIF-1α inhibitor topotecan than in rats that did not receive topotecan. Therefore, it may be assumed that the inhibition of the HIF-1α transcription factor 10 min before exposure to severe hypobaric hypoxia reduces skeletal muscle damage. The mechanisms that affect the adaptation of heart and skeletal muscles to hypoxia are discussed.