Abstract Syringodium isoetifolium was seagrass widely grown on the coast of Indonesia, and was the phytochemical source. This research was conducted to maximalize the extraction of their phytochemicals and bioactive compounds. Firstly, seagrass powder was extracted with different solvent polarities i.e. water, 50% ethanol, and 100% ethanol. Secondly, extraction was continued using different extraction techniques i.e. microwave-assisted extraction (MAE), ultrasound-assisted extraction (UAE-Bath system and UAE-Probe system), and conventional with the best solvent. Phytochemicals, bioactive compounds, antioxidant activity, and scanning electron microscope (SEM) were analyzed on the seagrass extracts. As result, the total phytochemical kind (i.e. terpene, polyphenols, alkaloid, and amino acid derivative groups) in the most dominant was had by 50% ethanol extract. Accordingly, extraction using the UAE-Probe with 50% ethanol as solvent able to obtain the richest bioactive compound, the most damaged cell microstructure, and the strongest antioxidant activity. Interestingly, quercetin was only detected dominant in UAE-Probe extract. Therefore, UAE-Probe with 50% ethanol solvent was the best method for recovering the valuable components in seagrass.