Metabolomics is a rapidly emerging discipline within functional genomics which is increasingly being applied to 19 understand biochemical phenotypes across a range of biological systems. Metabolomics measures all (or a 20 subset) metabolites in a cell at a specific time point, reflecting a snapshot of all the regulatory events responding 21 to the external environmental conditions. Although metabolomics and system biology approaches have been ap-22 plied to the study of terrestrial plants, few marine macrophytes have been examined using these novel technol-23 ogies. Marine macrophytes (including seaweeds and seagrasses) are marine ecosystem engineers delivering a 24 range of ecologically and economically valuable biological services; however they are under threat from a wide 25 range of anthropogenic stressors, climate variation, invasive species and pathogens. Investigating metabolomic 26 regulation in these organisms is crucial to understand their acclimation, adaptation and defence responses to 27 environmental challenges. This review describes the current analytical tools available to study metabolomics 28 in marine macrophytes, along with their limitations for both targeted and non-targeted workflows. To illustrate 29 recent advances in system biology studies in marine macrophytes, we describe how metabolites are used in 30 chemical defence to deter a broad range of invasive species and pathogens, as well as metabolomic 31 reprogramming leading to acclimation or adaptive strategies to environmental and anthropogenic stresses. 32 Where possible, the mechanistic processes associated with primary and secondary plant metabolism governing 33 cellular homeostasis under extreme environments are discussed. Functional integration of metabolomics with 34 the allied "omics" disciplines of transcriptomics and proteomics, as well as the emerging discipline of "fluxomics" 35 are discussed in the context of developing biological system networks, the identification of unknown gene/pro-36 tein functions and the analysis of metabolic pathways in marine plants exposed to stress. Finally, we provide a 37 comprehensive overview of an in silico plant metabolome database that can be utilized to advance our knowl-38 edge from a system biology approach to marine macrophytes.