Brachybacterium squillarum M-6-3(T) was isolated from salt-fermented seafood in Korea and belongs to the Dermabacteraceae, a rather isolated family within the actinobacterial suborder Micrococcineae. Here, we present the draft genome sequence of the type strain Brachybacterium squillarum M-6-3(T) (3,191,479 bp), a Gram-positive bacterium with high (72.8%) G+C content.