Anaerobic digestion, despite its preferable use as a treatment for high organic matter polluted waste streams, is susceptible to inhibitors, salt included. Therefore, two different experiments were conducted to observe the responses of bacterial and archaeal communities to hypersaline environments. In the first experiment, salt was added gradually, while in the second experiment, salt was added rapidly (so-called salt shocks were performed). The results of the gradual addition of salt showed a recovery of methane production after the salt concentration decreased. The NaCl concentration of 28.2 g/L seems to be the limit between stable operation and occurrence inhibition. The specific biogas production varied between 0.490 and 0.562 m3/kgtCOD during the stepwise salt addition, depending on the salt concentration, while the maximal achieved COD removal was 79.8%. The results of the rapid salt addition showed good recovery of the bacterial community, while a reduction of salt-sensitive species was observed in the archaeal community. The trend of specific biogas production during rapid salt addition was stable with an average value of 0.590 m3/kgtCOD, and it was observed that higher concentrations of up to 39.4 g/L of NaCl were tolerated. The maximum COD removal achieved during rapid salt addition was 83.1%. In conclusion, certain bacterial and archaeal communities were well-adapted to the hypersaline environment and remained active during the anaerobic digestion of substrates with high salt concentration.