Maize is a crop grown worldwide. Bacillus ciccensis 5L6^T was isolated from maize (Zea mays L., Jingke968) seeds and was a new species of Bacillus with potential anti-fungal activity. The complete genome of 5L6^T was sequenced and assembled with a length of 5,207,802 bp and a GC content of 37.42%. The proteins responsible for anti-fungal activity and the potential beneficial interaction with maize of 5L6^Twere annotated and reported here. The complete genome sequence of the new species B. ciccensis 5L6^T will promote its biological application.