We aimed to determine whether the composition of the fecal microbiota changes under hyperbaric conditions. In this study, we collected fecal samples from 6 healthy divers at three points during deep diving training (before, 2.1 MPa, end). The frequency of Clostridium cluster XVIII tended to be increased after compression. The frequencies of Clostridium cluster IV and subcluster XIVa were inversely correlated with that of Bacteroides. The compositional changes in the fecal microbiota exhibited interindividual variability. These findings suggest that hyperbaric conditions affect the fecal microbiota.