Streptomyces niveus SCSIO 3406 was isolated from a sediment sample collected from South China Sea at a depth of 3536 m. Four new sesquiterpenoid naphthoquinones, marfuraquinocins A-D, and two new geranylated phenazines, i. e. phenaziterpenes A and B, were isolated from the fermentation broth of the strain. Here, we present its genome sequence, which contains 7,990,492 bp with a G+C content of 70.46% and harbors 7088 protein-encoding genes. The genome sequence analysis revealed the presence of a 28,787 bp gene cluster encoding for 24 open reading frames including 1,3,6,8-tetrahydroxynaphthalene synthase and monooxygenase, seven phenazine biosynthesis proteins, two prenyltransferases and a squalene-hopene cyclase. These genes are known to be necessary for the biosynthesis of both marfuraquinocins and phenaziterpenes. Outside the gene cluster (and scattered around the genome), there are seven genes belonging to the methylerythritol phosphate pathway for the biosynthesis of the essential primary metabolite, isopentenyl diphosphate, as well as six geranyl diphosphate/farnesyl diphosphate synthase genes. The strain S. niveus SCSIO 3406 showed type I PKS, type III PKS and nonribosomal peptide synthetase cluster. The sequence will provide the genetic basis for better understanding of biosynthesis mechanism of the above mentioned six compounds and for the construction of improved strain for the industrial production of antimicrobial agents.