The bacterium Saccharothrix syringae NRRL B-16468 is the producer of nocamycin I and nocamycin II which feature tetramic acid and bicyclic ketal groups. In this study, we presented the complete genome of S. syringae NRRL B-16468 obtained from ARS Culture Collection. It contains a circular chromosome of 10,929,570 bp with an average GC content of 73.49%, 9316 genes, 12 rRNAs and 54 tRNAs. Bioinformatics analyses of the genome has demonstrated that it harbors 55 putative biosynthetic gene clusters (BGCs) involved in synthesizing diverse secondary metabolites. The backbones of the natural products synthesized by these BGCs encoding for type I polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and hybrid type I PKS-NRPS were analyzed, furthermore, the natural products synthesized by these BGCs with > 40% similarity to known BGCs were described in detail. The complete genome of S. syringae reveals its capacity in producing diverse bioactive natural products, and it will also shed lights on mining novel secondary metabolites from S. syringae through rational strategies.