We report the draft genome sequence of the promising fish probiotic Bacillus subtilis YBS29. This strain exhibits in vitro antimicrobial activity against Aeromonas veronii and enhances growth and disease resistance in the Indian major carp species Labeo rohita against motile Aeromonas septicemia (MAS). Its genome contains a gene cluster encoding multiple bacteriocins and lacks genes for virulence factors. These genomic features signify potential for safe use as a probiotic in aquaculture.