Background: Myoporum bontioides A. Gray, an evergreen shrub from the Myoporaceae family, is a commonly used medicinal plant. Many studies have been conducted on the biologically active constituents of whole parts of M. bontioides. However, the endophytes of M. bontioides have not been intensively investigated. A new chlorine-containing isocoumarin, named dichlorodiaportinol A (1) was isolated from the endophytic fungus Trichoderma sp. 09 isolated from the root of M. bontioides. Its cytotoxic activity against human breast cancer (MCF-7) and human liver cancer (HepG2) cell lines was evaluated. Materials and Methods: Different open silica gel column chromatographic techniques with different solvent systems were used for the separation of the constituents of the ethyl acetate extract of the culture broth of the endophytic fungus Trichoderma sp. 09. The structure of compound one was identified by analysis of spectroscopic data [one-dimensional (1D), two-dimensional (2D)-nuclear magnetic resonance (NMR), ultraviolet (UV), infrared (IR) and Mass spectrometry (MS)]. 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) assay method was used for the evaluation of cytotoxic activity of compound one against MCF-7 and HepG2 cell lines. Results: Compound one was identified as 3-(3,3-dichloro-2,3-dihydroxy-propyl)-8-hydroxy-6- methoxy-isochromen-1-one. It inhibited MCF-7 and HepG2 cell lines, with half maximal inhibitory concentration (IC 50 ) values of 17.8 and 39.6 μg/mL, respectively. Conclusions: Compound one is a new chlorine-containing isocoumarin with moderate cytotoxic activity against MCF-7 and HepG2 cell lines. Thus, endophytes of M. bontioides are worthy of consideration for the development and research of antitumor agents.