In the present study, the taxonomic position of Bacillus dafuensis and Bacillus massiliigabonensis was evaluated using genome-based comparison. The 16S rRNA gene sequence obtained from the Bacillus dafuensis FJAT-25496T genome showed 99.7% similarity with the type strain of Cytobacillus citreus, while Bacillus massiliigabonensis Marseille-P2639T showed 98.7% similarity with the type species of Cytobacillus solani. The 16S rRNA gene sequence similarity of Bacillus dafuensis FJAT-25496T and Bacillus massiliigabonensis Marseille-P2639T with Cytobacillus members was above the threshold (94.5%) for genus delineation. In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic (based on 71 bacterial single-copy genes) trees, Bacillus dafuensis and Bacillus massiliigabonensis clustered with Cytobacillus members. The 16S rRNA gene sequence, amino acid identity and percentage of conserved proteins analysis indicated Bacillus dafuensis FJAT-25496T and Bacillus massiliigabonensis Marseille-P2639T as a member of the genus Cytobacillus. The digital DNA–DNA hybridization and the average nucleotide identity values of Bacillus dafuensis FJAT-25496T and Bacillus massiliigabonensis Marseille-P2639T with Cytobacillus members was below the cut-off value (70/94%–95%) for species delineation. Based on the results we propose to transfer Bacillus dafuensis and Bacillus massiliigabonensis to the genus Cytobacillus as Cytobacillus dafuensis comb. nov., and Cytobacillus massiliigabonensis comb. nov., respectively.