Abstract The Bacillussp. isolate EB-40 was characterized in 'Prata Anã' banana (Musasp.) plants as an endophyte capable of colonizing both inter- and intracellular spaces of roots, nitrogen fixation, phosphate solubilization, in vitro synthesis of indole-3-acetic acid, and promotion of enhancements in the development of micropropagated banana seedlings. Here, we report the whole-genome sequence of Bacillus sp. isolate EB-40 and its taxonomic assignment. Its genome is composed of one chromosome and three plasmids. The chromosome is a circular double-stranded DNA (5,613,235 base pairs (bp) ) with a GC content of 35.3% and 5,462 genes. The three plasmids have a total length of 237,685 bp with 201 genes. Comparative genomics highlighted significant conservation of the isolate EB-40 genome with other B. cereus isolates, leading to its assignment it as a novel isolate within this species.