Three new thiodiketopiperazines, named phomazines A-C (1-3), along with 10 known analogues (4-13), were isolated from the fermentation broth of an endophytic fungus, Phoma sp. OUCMDZ-1847, associated with the mangrove plant Kandelia candel. The structures including the absolute configurations of the new compounds were unambiguously elucidated by spectroscopic, X-ray crystallographic, and Mosher's methods along with quantum ECD and (13)C NMR calculations. Compounds 2, 4, 5, 11, and 12 showed cytotoxicities against the HL-60, HCT-116, K562, MGC-803, and A549 cell lines with IC50 values in the range 0.05 to 8.5 μM.