Tetrodotoxin (TTX)-producing bacteria have attracted great interest as a model system for study of the TTX biosynthetic route. Here, we report the complete genome of the TTX-producing bacterium Bacillus sp. 1839. The genome of the strain Bacillus sp. 1839, previously isolated from the TTX-bearing marine ribbon worm Cephalothrix cf. simula, was obtained using second generation Illumina and third generation nanopore sequencing technologies. Phylogenetic analysis has classified this strain as Cytobacillus gottheilii.