Aims: Sabah’s red algae, Kappaphycus alvarezii is facing a problem whereby the production of seaweed is declining over the years due to a disease called ice-ice disease caused by Vibrio spp. Endophytic Bacillus strains have been widely studied for their potential as biocontrol agents against harmful pathogens. This study reports the genome sequence of the beneficial endophytic Bacillus strain VUMS1 isolated from the healthy K. alvarezii at Semporna Island in Sabah, attempting to determine its full biocontrol potential. Methodology and results : The whole genome sequence showed that VUMS1 genome size is 3,754,982 bp with 3,854 protein-coding where 2,535 are genes with assigned functions. The analysis revealed the presence of genes that are involved in antimicrobial and antifungal activity such as fengycin, bacillibactin, bacilysin and lichenysin. The biocontrol potential of VUMS1 was evaluated against Vibrio parahaemolyticus isolated from the diseased K. alvarezii. Results showed that the inhibition zone of VUMS1 by cross-streaking method against V. parahaemolyticus was 21 ± 0.71 mm and the growth of V. parahaemolyticus treated with VUMS1 in a co-culture experiment decreased by 98% on day 5 of treatment. Conclusion, significance and impact of study The results of this work indicate that VUMS1 is affiliated as Bacillus altitudinis and it may contribute to the biocontrol activity against Vibrio spp. infection in K. alvarezii. This is the first report of endophytic Bacillus altitudinis from K. alvarezii with biocontrol properties. Future studies will determine the potential application of the B. altitudinis VUMS1 strain in biological control and growth promotion for sustainable seaweed farming.