During periods of drainage, both water stress and oxygen can cause damage to indigenous methanogens. In the present study, we evaluated the tolerance of seven methanogenic strains (Methanobrevibacter arboriphilicus, Methanobacterium formicicum, Methanococcus vannielii, Methanospirillum hungatei, Methanoculleus olentangyi, Methanoplanus limicola, and Methanosarcina mazei) to long-term exposure to air/nitrogen and drying. We found that these methanogenic strains except for M. limicola and M. olentangyi in pre-dried cells offered more tenacious resistance to desiccation and oxygen exposure than those in enriched liquid cultures. In the case of M. formicicum, the liquid culture of this strain could remain viable when mixed well with fresh or sterile soil, but not when cultured without soil, or with agar slurry. These results suggest that indigenous methanogens localize within soil compartments to protect themselves from the damage caused by gradual drying under an oxic atmosphere.