Methanofervidicoccus sp. A16 is a novel thermophilic and obligate hydrogenotrophic methanogen isolated from a deep-sea hydrothermal vent chimney sample at the Mid Cayman spreading center, Caribbean Sea. Here we report the complete genome of strain A16, which has one circular chromosome of 1,485,358 bp with a mean G+C content of 35.01 mol%. The complete genome harbors 1442 predicted protein-encoding genes. Genes involved in hydrogenotrophic methane production and N 2 fixation were identified in this genome. This study expands our knowledge of methanogenesis at high temperatures and the involvement of these microorganisms in the carbon and nitrogen cycles of deep-sea hydrothermal environments.