•Agarivorans gilvus WH0801T was a novel species within the genus Agarivorans.•This is the first report on complete genome sequence of Agarivorans gilvus.•The bacterium could produce various agarases and catalyze the hydrolysis of agar.•Complete genome sequence of a single 4,416,600bp chromosome with a GC content of 45.9%.•Including 4279 protein-coding sequences, 22 rRNAs, 91 tRNAs and 9 miscellaneous RNAs. Agarivorans gilvus WH0801T, an agarase-producing bacterium, was isolated from the surface of seaweed. Here, we present the complete genome sequence, which consists of one circular chromosome of 4,416,600bp with a GC content of 45.9%. This genetic information will provide insight into biotechnological applications of producing agar for food and industry.