Red seaweed Sarcodia suae has various biological activities, but their chemical compositions have not been described in a broad spectrum. This study is to conduct a comprehensive analysis of Sarcodia suae metabolites using foodomics approach combining chromatography coupled with high resolution mass spectrometry (LC-HRMS) and structural-base classification for identification and screening of their potential bioactive metabolites. The seaweed samples were cultured and collected from two aquaculture systems in: (1) filtered running seawater (FR), and (2) recirculating aquaponics with tuna aquaculture (RA), respectively. The seaweed samples were dried and extracted using methanol-water, and methanol-chloroform-water extractions methods. The Q-Exactive Plus high-resolution orbitrap mass spectrometer was used to analyze compounds in both positive and negative electrospray mode and data-dependent acquisition (DDA) mode. The tandem mass spectra (MS/MS) were analyzed for chemical structure identification using ClassyFire. The number of compounds identified in two batches for the two cultured Sarcodia suae samples was 255 and 290, respectively. The reproducibility of two batches of extracted metabolites were 73.8 % and 74.4 % in FR and RA systems, respectively. According to structure-based classification for all identified compounds were organic acids and derivatives (25.8%), lipids and lipid-like molecules (22.1%), benzenoids (18.3%), organoheterocyclic compounds (17.1%), and other (16.6%). In conclusion, we used LC-HRMS-based foodomics approach to profile a comprehensive metabolome data and reveal differential metabolites between aquaculture systems. Bioactive potentials of extracted metabolites were discussed, and we assume that metabolites might be bioactive and can be studied and applied in food chemistry in further.