[Background] The Huixian wetland, located in the transition zone between the karst peak-cluster plain and karst depression area of Guilin city, is a typical karst wetland with a calcium-rich, alkalescent underground water supply. The sediment of the wetland is mostly free of oxygen, making it an ideal place to study novel species of anaerobic microbes. Hydrogenotrophic and acetoclastic methanogens play significant roles in the degradation of organic matter in the anaerobic environment; however, the physiology and ecology of microbial methanogenesis within the Huixian karst wetland is poorly understood. [Objective] To reveal the variation of archaeal communities, the functional groups of methanogens present, and the potential interactions among archaea from the sediment of the Huixian wetland under hydrogenotrophic and acetoclastic methanogenic conditions. [Methods] Sediment samples were incubated in anaerobic basal medium supplemented with hydrogen or acetate as the sole energy source. During incubation, the methane concentration in the headspace of the incubator was monitored. After 21 days of incubation, 3 libraries of nearly complete archaeal 16S rRNA gene sequences including 146 sequences and 3 mcrA (methyl-coenzyme reductase gene) libraries including 136 sequences from different samples were constructed. The dynamics of the archaeal communities in response to different conditions were studied through phylogenetic analysis. [Results] Methane was detected in the headspace of both H2- and acetate-enriched samples. The mcrA libraries were dominated by Methanosarcinales archaea consisting of four major phylogenetic branches: Zoige cluster I (ZC-I), anaerobic methanotrophic archaea of ANME-2d (AD), and the KT-I and KT-II subgroups. The branches of KT-I and KT-II were comparatively independent in the phylogenetic tree, with no previously reported sequences included, and these branches might represent novel subgroups of Methanosarcinales archaea. The composition of ZC-I, AD and KT-II increased by 45%–155% after incubation under methanogenetic conditions. Bathyarchaeota archaea accounted for 88%–100% of the 16S rRNA gene libraries. Most of the Bathyarchaeota came from the MCG-11 subgroup, which increased by 17% after incubation under acetic methanogenic conditions. [Conclusion] The sediment of the Huixian wetland contains novel archaeal sequences. The dominant hydrogenotrophic and acetoclastic methanogens within the wetland sediment are archaea of the Methanosarcinales order. Bathyarchaeota may play important roles in both in situ karst environments and methanogenic conditions.