This crossover study evaluated DNA methylation changes in human salivary samples following single sprint interval training sessions performed in hypoxia, with blood flow restriction (BFR), or with gravity-induced BFR. Global DNA methylation levels were evaluated with an enzyme-linked immunosorbent assay. Methylation-sensitive restriction enzymes were used to determine the percentage methylation in a part of the promoter of the gene-inducible nitric oxide synthase (p-iNOS), as well as an enhancer (e-iNOS). Global methylation increased after exercise (p < 0.001; dz = 0.50). A tendency was observed for exercise × condition interaction (p = 0.070). Post hoc analyses revealed a significant increase in global methylation between pre- (7.2 ± 2.6%) and postexercise (10.7 ± 2.1%) with BFR (p = 0.025; dz = 0.69). Methylation of p-iNOS was unchanged (p > 0.05). Conversely, the methylation of e-iNOS increased from 0.6 ± 0.4% to 0.9 ± 0.8% after exercise (p = 0.025; dz = 0.41), independently of the condition (p > 0.05). Global methylation correlated with muscle oxygenation during exercise (r = 0.37, p = 0.042), while e-iNOS methylation showed an opposite association (r = -0.60, p = 0.025). Furthermore, p-iNOS methylation was linked to heart rate (r = 0.49, p = 0.028). Hence, a single sprint interval training increases global methylation in saliva, and adding BFR tends to increase it further. Lower muscle oxygenation is associated with augmented e-iNOS methylation. Finally, increased cardiovascular strain results in increased p-iNOS methylation.