The genome sequence of *Bacillus cereus* and comparative analysis with *Bacillus anthracis* reveals insights into the genetic relationships and evolutionary history of these closely related bacteria. *B. cereus* is an opportunistic pathogen that causes food poisoning, while *B. anthracis* is a human and animal pathogen and a potential biological weapon. *B. thuringiensis* is an insect pathogen used as a pesticide. Although *B. anthracis* and *B. thuringiensis* can be distinguished from *B. cereus* by the presence of specific toxins and capsules, phylogenetic studies based on chromosomal genes have produced conflicting results regarding whether these three species are variants of the same species or different species. The complete genome sequence of *B. cereus* ATCC 14579 and the gapped genome of *B. anthracis* A2012 were analyzed to identify conserved and unique genes between the two species. These analyses help clarify the phylogeny of the *cereus* group and identify plasmid-independent species-specific markers. The genome of *B. cereus* ATCC 14579 has a total length of 4.3 Mb, with a GC content of 35.3%. It contains a linear plasmid of approximately 15.1 kb, which is homologous to a type B DNA polymerase found in *B. subtilis* phage Φ29 and several linear mitochondrial plasmids. The plasmid also contains a gene homologous to an endolysin, suggesting it may be a linear plasmid or prophage. Phylogenetic analysis of the *cereus* group shows that *B. cereus* ATCC 14579 and *B. anthracis* strains are not particularly close, and their ecological niches are very different. However, 4,505 CDSs in *B. cereus* ATCC 14579 have 80–100% identity to their homologues in *B. anthracis* A2012. The average identity for this group of genes is 92.1%. The large core set of genes (75–80%) conserved between *B. cereus* and *B. anthracis* could have been inherited from a common ancestor. However, the metabolic potential of the core set contradicts the hypothesis that the common ancestor was a soil bacterium. Instead, the bacteria appear to have evolved to utilize proteins, peptides, and amino acids as preferred nutrients. The core set of genes includes numerous factors for invasion, establishment, and propagation of bacteria within the host. *B. cereus* ATCC 14579The genome sequence of *Bacillus cereus* and comparative analysis with *Bacillus anthracis* reveals insights into the genetic relationships and evolutionary history of these closely related bacteria. *B. cereus* is an opportunistic pathogen that causes food poisoning, while *B. anthracis* is a human and animal pathogen and a potential biological weapon. *B. thuringiensis* is an insect pathogen used as a pesticide. Although *B. anthracis* and *B. thuringiensis* can be distinguished from *B. cereus* by the presence of specific toxins and capsules, phylogenetic studies based on chromosomal genes have produced conflicting results regarding whether these three species are variants of the same species or different species. The complete genome sequence of *B. cereus* ATCC 14579 and the gapped genome of *B. anthracis* A2012 were analyzed to identify conserved and unique genes between the two species. These analyses help clarify the phylogeny of the *cereus* group and identify plasmid-independent species-specific markers. The genome of *B. cereus* ATCC 14579 has a total length of 4.3 Mb, with a GC content of 35.3%. It contains a linear plasmid of approximately 15.1 kb, which is homologous to a type B DNA polymerase found in *B. subtilis* phage Φ29 and several linear mitochondrial plasmids. The plasmid also contains a gene homologous to an endolysin, suggesting it may be a linear plasmid or prophage. Phylogenetic analysis of the *cereus* group shows that *B. cereus* ATCC 14579 and *B. anthracis* strains are not particularly close, and their ecological niches are very different. However, 4,505 CDSs in *B. cereus* ATCC 14579 have 80–100% identity to their homologues in *B. anthracis* A2012. The average identity for this group of genes is 92.1%. The large core set of genes (75–80%) conserved between *B. cereus* and *B. anthracis* could have been inherited from a common ancestor. However, the metabolic potential of the core set contradicts the hypothesis that the common ancestor was a soil bacterium. Instead, the bacteria appear to have evolved to utilize proteins, peptides, and amino acids as preferred nutrients. The core set of genes includes numerous factors for invasion, establishment, and propagation of bacteria within the host. *B. cereus* ATCC 14579