Nocardia sp. strain CS682 is a rare actinobacterium with a promising ability to produce secondary metabolites such as nargenicin A1 (an effective antibacterial compound) and IBR-3 (a UV-protectant molecule). Here, we report the complete genome sequence of Nocardia sp. CS682, obtained by PacBio sequencing as a single contig with 8,919,230 bp (GC content, 63.3%).