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Securing new sources of renewable energy and achieving national self-sufficiency in natural gas have become increasingly important in recent times. The study described in this paper focuses on three geologically diverse underground gas reservoirs (UGS) that are the natural habitat of methane-producing archaea, as well as other microorganisms with which methanogens have various ecological relationships. The objective of this research was to describe the microbial metabolism of methane in these specific anoxic environments during the year. DNA sequencing analyses revealed the presence of different methanogenic communities and their metabolic potential in all sites studied. Hydrogenotrophic <i>Methanobacterium</i> sp. prevailed in Lobodice UGS, members of the hydrogenotrophic order <i>Methanomicrobiales</i> predominated in Dolní Dunajovice UGS and thermophilic hydrogenotrophic members of the <i>Methanothermobacter</i> sp. were prevalent in Tvrdonice UGS. Gas composition and isotope analyses were performed simultaneously. The results suggest that the biotechnological potential of UGS for biomethane production cannot be neglected.