Using the one strain many compounds (OSMAC) strategy and guided by LC-MS results, we explored the metabolites of marine algae-derived strain Streptomyces thermolineatus NAK03196 and discovered a new class of molecules with an unexpected skeleton, chlorobactine A (1). Its structure was determined by 1D and 2D NMR spectroscopy, HR-ESI-MS, single-crystal X-ray diffraction analysis (Cu Kα), and ECD calculation. Chlorobactine A (1) contains dichlorine atoms and possesses a unique [6/6/6] tricyclic fused skeleton structure. Meanwhile, a plausible biosynthetic pathway for 1 was proposed based on the molecular structures and bioinformatic analysis.