Background: Syringodium isoetifolium is a seagrass that grows abundantly in Indonesian territorial waters and has been known to be of high significance not only for the seawater ecosystem, but also for human beings (as food, nutritional and pharmaceutical products). In this study, the bioactive constituent of Syringodium isoetifolium was extracted using several different techniques to recover a maximum yield. Methods: Extraction was carried out by conventional and non-conventional (Microwave-assisted extraction, ultrasound-assisted extraction-bath system, and ultrasound-assisted extraction- (UAE) probe system) techniques with green solvents (water, 50% ethanol, and 100% ethanol). Results: As a result, 50% ethanol and water extracts exhibited a significantly higher yield. Total phenol content was significantly higher for 50% ethanol extract. Different extraction techniques (using 50% ethanol solvent) showed that the UAE-probe was the best technique since it yielded the highest total phenol (17.37 ± 2.16 mg GAE/g) and the richest bioactive compounds (Choline, betaine, 3,5-di-tert-butyl-4-hydroxybenzoic acid, 7-Hydroxycoumarine, 4-Methoxycinnamic acid, Zearalenone, Caffeic acid, Levalbuterol, Phloretin, Dihydrocaffeic acid, Quercetin-3β-D-glucoside and Quercetin). Interestingly, choline was the most abundant compound in the extract obtained with different extraction techniques. In this in silico assay, choline from seagrass extract was shown as an anti-inflammatory. The interaction pathway of the choline compound with receptors (TNF-α, IL-1β, and IL6) had a higher binding affinity value than the inhibitor-receptor interaction (i.e. -3.4, -3.0, and -2.8 kcal/mol). The cytotoxicity test on TIG-1 cells showed that the extract did not have a toxic effect on them. Conclusions: These findings support the potential use of Syringodium isoetifolium as a bioactive food ingredient.