Background　Bacteria　are　an　essential　component　of　the　earth`s　biota　and　affect　circulation　of　matters　through　their　metabolic　activity.　They　also　play　an　important　role　in　the　carbon　and　nitrogen　cycle　in　the　deep-sea　environment.　In　this　paper,　two　strains　from　deep-sea　sediments　were　investigated　in　order　to　understand　nitrogen　cycling　involved　in　the　deep-sea　environment.　Results　In　this　paper,　the　basic　genomic　information　of　two　strains　was　obtained　by　whole　genome　sequencing.　The　Cobetia　amphilecti　N-80　and　Halomonas　profundus　13　genome　sizes　are　4,160,095　bp　with　a　GC　content　of　62.5%　and　5,251,450　bp　with　a　GC　content　of　54.84%.　Through　a　comparison　of　functional　analyses,　we　predicted　the　possible　C　and　N　metabolic　pathways　of　the　two　strains　and　determined　that　Halomonas　profundus　13　could　use　more　carbon　sources　than　Cobetia　amphilecti　N-80.　The　main　genes　associated　with　N　metabolism　in　Halomonas　profundus　13　are　narG,　narY,　narI,　nirS,　norB,　norC,　nosZ,　and　nirD.　On　the　contrast,　nirD,　using　NH4+　for　energy,　plays　a　main　role　in　Cobetia　amphilecti　N-80.　Both　of　them　have　the　same　genes　for　fixing　inorganic　carbon:　icd,　ppc,　fdhA,　accC,　accB,　accD,　and　accA.　Conclusion　In　this　study,　the　whole　genomes　of　two　strains　were　sequenced　to　clarify　the　basic　characteristics　of　their　genomes,　laying　the　foundation　for　further　studying　nitrogen-metabolizing　bacteria.　Halomonas　profundus　13　can　utilize　more　carbon　sources　than　Cobetia　amphilecti　N-80,　as　indicated　by　API　as　well　as　COG　and　KEGG　prediction　results.　Finally,　through　the　analysis　of　the　nitrification　and　denitrification　abilities　as　well　as　the　inorganic　carbon　fixation　ability　of　the　two　strains,　the　related　genes　were　identified,　and　the　possible　metabolic　pathways　were　predicted.　Together,　these　results　provide　molecular　markers　and　theoretical　support　for　the　mechanisms　of　inorganic　carbon　fixation　by　deep-sea　microorganisms.