The interest in photoplethysmography (PPG) for sleep monitoring is increasing because PPG may allow assessing heart rate variability (HRV), which is particularly important in breathing disorders. Thus, we aimed to evaluate how PPG wearable systems measure HRV during sleep at high altitudes, where hypobaric hypoxia induces respiratory disturbances. We considered PPG and electrocardiographic recordings in 21 volunteers sleeping at 4554 m a.s.l. (as a model of sleep breathing disorder), and five alpine guides sleeping at sea level, 6000 m and 6800 m a.s.l. Power spectra, multiscale entropy, and self-similarity were calculated for PPG tachograms and electrocardiography R-R intervals (RRI). Results demonstrated that wearable PPG devices provide HRV measures even at extremely high altitudes. However, the comparison between PPG tachograms and RRI showed discrepancies in the faster spectral components and at the shorter scales of self-similarity and entropy. Furthermore, the changes in sleep HRV from sea level to extremely high altitudes quantified by RRI and PPG tachograms in the five alpine guides tended to be different at the faster frequencies and shorter scales. Discrepancies may be explained by modulations of pulse wave velocity and should be considered to interpret correctly autonomic alterations during sleep from HRV analysis.