This thesis described the chemical investigations of natural products from Australian marine sponge-derived fungi. Sponge samples were collected from the Great Barrier Reef, Queensland, Australia, by Queensland Museum. The thesis is divided into eight chapters and can be devided into two major parts. The first three chapters comprised the first part of the thesis: Chapter 1 outlined the research background, literature review of marine fungal secondary metabolites; Chapter 2 introduced fungal culture and storage background knowledge, and the list of isolated marine fungal strains. Chapter 3 introduced the background of the thrombin inhibition assay and assay results. The second part (Chapter 4 to 7) of this thesis is focused on chemical isolation and structure elucidation of secondary metabolites from isolated fungal strains, mostly active strains against thrombin. An unidentified fungal strain, FS-G315858 (T)-Y, isolated from the frozen sponge sample Dysidea sp.1400 produced five peptide compounds (chapter 4, 16-20). Compound 16 is a polypeptide which features the same relative configuration with a known compound unguisine A, and compounds 17-20 are diketopiperazines. Active fungal strains FS-G315695 (T)-Y and FDPS-61732-YB were isolated from different sponge samples. However, they were identified to be the identical fungal strain Eurotium rubrum; the chemical isolation of FS-G315695 (T)-Y from its mycelia EtOAc extract resulted in three compounds (chapter 5, 17-19). Compounds 18 and 19 were identified to be flavoglaucin and iso-dihydroauroglaucin. Compound 17 was identified to have the same relative configuration with a known compound neo-echinulin A. The chemical isolation of FDPS-61732-YB from its broth EtOAc extract resulted in several diketopiperazines (chapter 5, 27-29). Another active fungal strain FS-G315695 (T)-WY was identified as Aspergillus ochraceous, the chemical isolation of its mycelia EtOAc extract resulted in one benzodiazepine compound (chapter 6, 18), together with two fatty acids (chapter 6, 16-17). The structure of compound 18 was elucidated and identified to have same relative configuration with the known compound circumdatin E. Media comparison for active fungal strain FS-G315695 (T)-Y was conducted and this work resulted in producing several neo-echinulin analogues (chapter 7, 1-3). The isolation and structure elucidation of these compounds were reported in chapter 7.