Sulfitobacteris one of the major sulfite-oxidizing alphaproteobacterial groups and is often associated with marine algae and corals. Their association with the eukaryotic host cell may have important ecological contexts due to their complex lifestyle and metabolism. However, the role ofSulfitobacterin cold-water corals remains largely unexplored. In this study, we explored the metabolism and mobile genetic elements (MGEs) in two closely relatedSulfitobacter faviaestrains isolated from cold-water black corals at a depth of ~1000 m by comparative genomic analysis. The two strains shared high sequence similarity in chromosomes, including two megaplasmids and two prophages, while both contained several distinct MGEs, including prophages and megaplasmids. Additionally, several toxin-antitoxin systems and other types of antiphage elements were also identified in both strains, potentially helpingSulfitobacter faviaeovercome the threat of diverse lytic phages. Furthermore, the two strains shared similar secondary metabolite biosynthetic gene clusters and genes involved in dimethylsulfoniopropionate (DMSP) degradation pathways. Our results provide insight into the adaptive strategy ofSulfitobacterstrains to thrive in ecological niches such as cold-water corals at the genomic level.