Variibacter gotjawalensis GJW-30T is a gram-negative, strictly aerobic bacterium to form pleomorphic. Here we present the 4.5-Mb genome sequence of the type strain of V. gotjawalensis GJW-30T, which consists a chromosome for the total 4,586,237bp with a G+C content of 62.2mol%. This is the first report of the full genome sequence of a species of the novel genus Variibacter isolated from Gotjawal, a unique area in Jeju, Republic of Korea.