A new xanthone derivative, 3,5,8-trihydroxy-2,2-dimethyl-3,4,4-trihydro-2H,6H-pyrano[3,2-b]-xanthen-6one (1), together with three known compounds, 5,8-dihydroxy-2,2-dimethyl-2H,6H-pyrano[3,2-b]xanthen6-one (2), cyclo-(N-O-methyl-L-Trp-L-Ile-D-Pip-L-2-amino-8-oxo-decanoyl) (3), and cyclo-(Phe-Tyr) (4), was isolated from the mangrove endophytic fungus No. ZSU-H16 obtained from the South China Sea coast. Their structures were elucidated by spectroscopic methods, mainly 1D and 2D NMR spectroscopic techniques. Compound 1 exhibited cytotoxicity against KB and KBV 200 cells with IC50 values greater than 50 μg/mL, respectively.