Streptomyces sp. SCSIO 03032, isolated from a deep-sea sediment sample (-3412 m) from the Indian Ocean, produces several classes of bioactive compounds including alpha-pyridone antibiotics (piericidins), polycyclic macrolactams (heronamides) and bisindole alkaloids (spiroindimicins, indimicins and lynamicins). Here we report the complete genome sequence of Streptomyces sp. SCSIO 03032, which consists of a 6,287,975 bp linear chromosome. The genome analysis reveals the presence of 29 putative biosynthetic gene clusters for secondary metabolites, including those for piericidins, heronamides and spiroindimicins/indimicins/lynamicins. The genome sequence suggests that Streptomyces sp. SCSIO 03032 could be a producer for novel bioactive natural products with potential applications in drug discovery.