Metabolomic methods can be utilised to screen diverse biological systems for potentially novel and sustainable sources of antibiotics and pharmacologically-active drugs. Marine sponges and their endosymbionts have proven to be abundant sources of bioactive compounds. HR-LCFTMS and NMR were used in the identification of compounds isolated from a marine bacterium and its host sponge, as well as in the dereplication and metabolic profiling of other sponge-associated bacteria.24-Methylenecholesterol and two novel steroids, 24-vinyl-cholest-9-ene-3β,24-diol and 20-methyl-pregn-6-en-3β-ol, 5α,8α-epidioxy, all significantly active against Trypanosoma brucei and moderately active against Mycobacterium marinum were isolated from the Irish Sea sponge Haliclona simulans. Extracts from SM8, the Streptomyces sp. isolated from H. simulans demonstrated antibacterial and antifungal activities. NMR spectroscopy identified the major components of the antibacterial fractions as polyhydroxylated saturated fatty acids. HR-LCFTMS assisted in identifying members of the antimycin A family in the antifungal fractions. This was further confirmed using gene knockout studies. Three butenolides were also isolated from the SM8 extracts.HR-LCFTMS was applied to the dereplication of extracts from bacteria from marine sponges. EG4, a Microbacterium sp. isolated from Callyspongia aff. implexa, was selected and its cultivation optimised from small scale to larger scale production, under different media conditions, with the aid of metabolomic methods and multivariate analysis to identify and trace biomarkers. In addition, several compounds that were active against T. brucei and M. marinum and Nocardia farcinica were isolated and identified.Metabolomics has become a powerful tool in systems biology which allows us to gain insights into the potential of natural marine isolates for synthesis of significant quantities of promising new agents, and allows us to manipulate the environment within fermentation systems in a rational manner to select the desired bioactive metabolome.