The types and volumes of bioactive compounds can vary in plants that inhabit different areas. This research aimed to map and analyze the content of bioactive compounds in the seagrass Enhalus acoroides in the waters around Morotai Island. The study was conducted from June to August 2024, with sampling points spread across six sub-districts: Pilowo and Waringin Villages (South Morotai), Sambiki Tua and Sangowo Villages (East Morotai), Tanjung Saleh and Gorua Villages (North Morotai), Pangeo and Sopi Villages (Morotai Jaya), Usbar Pantai and Wayabula Villages (West South Morotai), and Posi-Posi and Saminyamau Villages (Rao Island). The extraction and identification of bioactive compounds from the seagrass were performed at the Faculty of Fisheries and Marine Science Laboratory. Seagrass mapping was conducted using ArcGIS software. The identification of bioactive compounds was carried out qualitatively using chemical detectors, including alkaloids, flavonoids, saponins, steroids, triterpenoids, phenols, and quinones. The results indicate that Enhalus acoroides is found in the waters of Morotai Island, specifically in the districts of South Morotai (Pilowo and Waringin), South West Morotai (Wayabula), Rao Island (Posi-Posi and Saminyamau), East Morotai (Sangowo and Sambiki Tua), and North Morotai (Tanjung Saleh). The yield of Enhalus acoroides leaf extract was 61.17%, higher than the rhizome yield of 48.28%. Among the accessions, the highest yield of Enhalus acoroides extract was from the Wayabula accession (19.84%), while the lowest was from the Saminyamau accession (1.72%). The methanol extract of Enhalus acoroides contains bioactive compounds, including alkaloids, saponins, steroids, triterpenoids, phenols, and quinones.