Methane is produced in the foregut (rumen) of ruminants by methanogens, which act as terminal reducers of carbon in the rumen system. The multistep methanogenesis pathway is well elucidated, mainly from the study of non-rumen methanogens, but the adaptations that allow methanogens to grow and persist in the rumen are not well understood. The Pastoral Greenhouse Gas Research Consortium is sequencing the genome of Methanobrevibacter ruminantium, a prominent methanogen in New Zealand ruminants, as part of a project to mitigate greenhouse gases. The genome is ~3.0 Mb in size with a guanine–cytosine (GC) content of 33.68%. All of the components of the methanogenesis pathway have been identified and comparison of these gene sequences with those from Methanothermobacter thermoautotrophicus and Methanosphaera stadtmanae indicates that methanogenesis gene organisation is conserved within the Methanobacteriales. The genome of M. ruminantium contains a prophage sequence (designated φmru) with distinct functional modules encoding phage integration, DNA replication and packaging, capsid proteins and lysis functions. A low GC region found at the distal end of the phage sequence harbours a putative DNA restriction/modification system which might provide additional protection against foreign DNA. The genome also contains many large surface proteins with characteristics that indicate that they may mediate association with other rumen microbes. Approximately half of the genes identified within the genome have no known function. Determining the function of these new genes will assist in defining the role of M. ruminantium in methane formation in the rumen and help identify means to control methane emissions from ruminant animals.