Although the recent years have witnessed a growing interest in functional connectivity (FC) through brain sources, the FC in extreme situations has not been completely elucidated. This paper is aimed at investigating whether the expertise acquired during the deep-sea diving is reflected in FC in a group of professional divers (PDs) compared to a group of new divers (NDs), and how it could affect the concentration and stress levels. The sources of brain frequency rhythms, derived by the electroencephalography acquisition in a hyperbaric chamber, were extracted in different frequency bands and the corresponding FC was estimated in order to compare the two groups. The results highlighted a significant decrease of the alpha source in PDs during air breathing and a significant increase of the upper beta source over central areas at the beginning of post-oxygen air, as well as an increase of beta FC between fronto-temporal regions in the last minutes of oxygen breathing and in the early minutes of post-oxygen air. This provides evidence in support of the hypothesis that experience and expertise differences would modulate brain networks. These experiments provided the unique opportunity of investigating the impact of the neurophysiological activity in simulated critical scenarios in view of the investigation in real sea-water experiments.