Diseases of the commercially cultivated brown seaweed Saccharina japonica have been noticed since the 1960s in China. However, the usually opportunistic nature of the pathogenic bacteria of seaweeds is still a main obstacle for isolating and identifying pathogenic bacteria responsible for causing diseases of the cultivated S. japonica. In this study, a Gram-positive bacterium XP-2 was isolated from the abnormal diseased mature sporophytes of S. japonica. Pathogenicity test indicated that XP-2 could cause green-rotten disease in healthy juvenile sporophytes and significant algal ultrastructural changes were observed after S. japonica was infected by XP-2. The cells shrank, and the thylakoids of the chloroplasts became blurred after 12 h of re-infection. At 24 h slight deformation was observed in the structure of the mitochondria, chloroplasts, and nucleus. There also were many vacuoles in the infected cells. After 31 h of re-infection, mitochondrial structure and thylakoids became more indistinct. SEM and TEM observations indicated that XP-2 was rod-shaped with no flagella. Analysis of the full length 16S rRNA gene sequence and physiological and chemical characteristics indicated that XP-2 was closely related to Exiguobacterium oxidotolerans 12280 T. Based on these results, XP-2 was designated Exiguobacterium oxidotolerans XP-2. The pathogenicity of E. oxidotolerans XP-2 was identified by Koch’s Postulate under laboratory conditions. These results enrich the growing list of pathogenic bacteria in commercially cultivated seaweeds and also provide a foundation for investigating the virulence mechanisms of pathogenic bacteria of commercially cultivated seaweeds in the near future.