Bacillus frigoritolerans JHS1 was isolated from the soil of a tomato plant (Solanum lycopersicum). The genome consists of one circular chromosome (5,552,463 bp) and a plasmid (16,118 bp) with an overall GC content of 40.57%. Using TYGS for taxonomic classification, strain JHS1 was assigned to the species Bacillus frigoritolerans.