Understanding the mechanisms of oxygen supply regulation, which involves the respiratory and cardiovascular systems, during human adaptation to intense physical activity, accompanied by hypoxemia, is important for the management of a training process. The objectives of this study were to investigate the cardiorespiratory coherence (CRC) changes in the low-frequency band in response to hypoxic exposure and to verify a dependence of these changes upon sports qualification level in athletes. Twenty male runners aged 17-25 years were exposed to acute normobaric hypoxia (10% O 2) for 10 min. Respiration, gas exchange, and heart rate were measured at baseline, during hypoxia, and after the exposure. To evaluate cardiorespiratory coupling, squared coherence was calculated based on 5-s averaged time series of heart and respiratory rhythms. Based on sports qualification level achieved over 4 years after the experimental testing, athletes were retrospectively divided into two groups, one high level (HLG, n = 10) and the other middle level (MLG, n = 10). No differences in anthropometric traits were observed between the groups. In the pooled group, acute hypoxia significantly increased CRC at frequencies 0.030-0.045 Hz and 0.075 Hz. In response to hypoxia, oxygen consumption decreased in HLG, and carbon dioxide production and ventilation increased in MLG. At 0.070-0.080 Hz frequencies in hypoxia, the CRC in HLG was higher than in MLG. Thus, highly qualified athletes enhance intersystem integration in response to hypoxia. This finding can be a physiological sign for the prognosis of qualification level in runners.