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Unexpected atypical isolates of <i>Bacillus cereus s.l.</i> occasionally challenge conventional microbiology and even the most advanced techniques for anthrax detection. For anticipating and gaining trust, 65 isolates of <i>Bacillus cereus s.l.</i> of diverse origin were sequenced and characterized. The BTyper3 tool was used for assignation to genomospecies <i>B. mosaicus</i> (34), <i>B. cereus s.s</i> (29) and <i>B. toyonensis</i> (2), as well as virulence factors and toxin profiling. None of them carried any capsule or anthrax-toxin genes. All harbored the non-hemolytic toxin <i>nheABC</i> and sphygomyelinase <i>spH</i> genes, whereas 41 (63%), 30 (46%), 11 (17%) and 6 (9%) isolates harbored <i>cytK-2</i>, <i>hblABCD</i>, <i>cesABCD</i> and at least one insecticidal toxin gene, respectively. Matrix-assisted laser desorption ionization-time of flight mass spectrometry confirmed the production of cereulide (<i>ces</i> genes). Phylogeny inferred from single-nucleotide polymorphisms positioned isolates relative to the <i>B. anthracis</i> lineage. One isolate (BC38B) was of particular interest as it appeared to be the closest <i>B. anthracis</i> neighbor described so far. It harbored a large plasmid similar to other previously described <i>B. cereus s.l.</i> megaplasmids and at a lower extent to pXO1. Whereas bacterial collection is enriched, these high-quality public genetic data offer additional knowledge for better risk assessment using future NGS-based technologies of detection.