Natural products possessing the 3-(furan-2(5H)-ylidene)furan-2,4(3H,5H)-dione (furylidene tetronic acid) skeleton are rare and were encountered only as fungal metabolites. The configurational assignment of the furylidene tetronic acid core using conventional approaches remained a challenge. Pestalotic acids A–G (1–7) are new furylidene tetronic acid derivatives isolated from a plant endophyte Pestalotiopsis yunnanensis. The structure of 1 was elucidated by combination of NMR experiments, X-ray crystallography, and ECD calculations. Compounds 3 and 7 showed significant antimicrobial activity.