This study reveals the complete genome sequences obtained through whole-genome shotgun sequencing (WGS) of two Algerian Bacillus strains which were selected as biocontrol agents of Zymoseptoria tritici, the causal agent of septoria tritici blotch of wheat. By previous analyses, based on the 16S rRNA identification, the novel strains, termed Alg.24B1 and Alg.24B2, were identified as Bacillus subtilis and Bacillus simplex, respectively. The MLST classification confirmed the identification of Alg.24B1 as Bacillus subtilis and the identification of Alg.24B2 as Peribacillus simplex. The first analyses of these two strains reveal the production of secondary metabolites involved in the suppressing process of the target fungal phytopathogen. Further, greater perceptions of the biocontrol mechanisms of these Bacillus strains will be conducted using WGS as a more efficient and reliable approach.