Although flight phobia is very common in the general population, knowledge of the underlying mechanisms is limited. The aim of the current study is to determine whether hypoxia is selectively associated with flight anxiety. We wanted to explore levels of oxygen saturation (SpO2) and the associated subjective somatic sensations in flight phobics and controls. The data collected in this study were obtained from 103 participants: 54 had flight phobia, 49 were controls. SpO2 as well as a subjective report of somatic sensations and anxiety were measured during short haul flights, both at ground level and at cruising altitude. Results indicated that both flight phobics and controls showed a comparable clinical significant decrease in SpO2 from sea level to cruising altitude. Next, at ground level the flight phobic group reported more somatic sensations, most likely due to the elevated levels of anxiety at that point. However, at cruising altitude the flight phobic group still reported more somatic sensations while the level of anxiety was no longer significantly different from controls. This finding points to altered symptom perception in flight phobia and stresses the importance of somatic sensations in this particular phobia.