A total of 178 fungal isolates were successfully isolated from marine invertebrates collected in surrounding waters of Pulau Redang and Pulau Payar, Malaysia. All isolates grew on both sea water and non-sea water media, thus all of them can be classified as facultatively marine. No obligate marine fungal were isolated. A number 25 extracts (43.9%) were found to be potentially active by inhibiting >50% of the growth of the P388 cells. Of these, 10 extracts (40%) showed cytotoxicity (IC,„ <12,500 mg/ml) against the P388 cell lines. HPLC screening using in-house HPLC-UV/Rt library database readily dereplicated four known secondary metabolites from four cytotoxic fungal extracts, while six extracts contained peak(s) that were not readily dereplicated. These metabolites were dereplicated from extracts F6406 (meleagrine), F6415 (cytochalasins), F6430 (indole-3-carboxylic acid) and F6451 (dehydrosterigmatocystin). The results showed naturally occurring metabolites in Malaysian marine fungi have potentials to produce cytotoxic metabolites enabling the discovery of new bioactive compounds, hence merit future studies.