The discovery of new secondary metabolites from plants and endophytes has become more challenging in natural products chemistry. Different approaches have been applied in order to increase the production of bioactive metabolites from microbial sources. Bacteria and fungi interact within the host plant and stimulate competition for nutrients and spaces which is regarded as a major ecological factor that induces production of bioactive secondary metabolites. Prior to this study, metabolomics has been applied to identify and preliminarily screen the production of bioactive secondary metabolites from three strains: A. aculeatus, L. theobromae, and Fusarium sp. inoculated in both solid rice and liquid culture media at different growth stages 7, 15 and 30 days. High resolution mass spectrometry and NMR spectroscopy were used as metabolomics profiling tools. The spectral data was processed by utilizing the quantitative expression analysis software Xcalibur, Mzmine 2.10, in house MS-Excel macro coupled with Antimarin (Antibase and Marinlit) and Dictionary of Natural Products databases for dereplication studies. SIMCA P+ 13.0 was used to prove that the optimized models were statistically sound. In this study, isolation and fractionation of bioactive natural products was done on the crude organic extract of the mangrove plant Avicennia lanata by using several high-throughput chromatographic techniques which yielded three new derivatives of naphthofuranquinone along with three known congeners, triterpenes and sterol compounds. Meanwhile, four pure endophytic fungal strains were also isolated from the root, stem, stem barks and leaf parts of A. lanata. The fungi were identified by DNA extraction, PCR amplification and sequencing by using polymerase chain reaction (PCR) and the universal ITS primers. The voucher specimens of all strains were deposited in Natural Product Metabolomics Laboratory (SIPBS, University of Strathclyde). The isolated endophytic fungi from the mangrove plant A. lanata were identified as Aspergillus aculeatus obtained from the leaf part; Lasiodiplodia theobromae from the stem; Aspergillus flavipes from the stem bark and Fusarium sp. from the root part. Metabolomic profiling of Fusarium sp. extract from the 15-days solid culture (FRC15) yielded four 1,4-naphthoquinone with naphthazarin structures and ergosterol peroxide. Meanwhile, isolation work of bioactive metabolites on the crude extract of a 30 day solid rice culture of A. aculeatus afforded two new metabolites, aspergillusenone and 2-(3,4-dihydroxyphenyl)-N,N-dimethylacetamide, along with four known simple phenolics, secalonic acid A and ergosterol peroxide. The investigation for other potential bioactive compounds was carried out on the endophytic fungus L. theobromae grown on the 15-day solid rice culture (LTRC15) which produced mellein along with its three derivatives and two other phenolic compounds. Structure elucidation of the isolated secondary metabolites was established using 1D and 2D-NMR and HRESI-MS.Except for taraxerone, taraxerol, stigmasterol and β-sitosterol, all isolated compounds from the mangrove plant A. lanata and its fungal endophyte showed significant anti-trypanosomal activity to T. b. brucei. In this study, it proved that metabolomics approach is an essential tool to identify biomarkers from mangrove plant and its endophytic fungi to target the isolation of potential anti-trypanosomal effective drugs.