The Biodiversity Assessment of Seagrass Ecosystem in Orwer and Ambroben Waters, Biak Numfor Regency, Papua Province is very important for a baseline study of the ecosystem health of seagrass beds. The ecological function of seagrass ecosystems is to stabilize the seabed, provide food and habitat for other marine life, and maintain water quality. The research conducted aims to (1) determine the types of seagrasses, density, and percentage of seagrass cover in Orwer and Ambroben waters, and (2) find out the characteristics of aquatic environmental parameters that play an important role in determining the health status of seagrass meadow ecosystems. Based on the results of the research has been found as many as four types of seagrasses are in Orwer waters, namely Halodule pinifolia, Cymodocea rotundata, Thalassia hemprichii, and Halophila ovalis. In Ambroben waters have been found as many as 7 types of seagrass, namely Halodule pinifolia, Halodule uninervis, Cymodocea rotundata, Syringodium isoetifolium, Enhalus acoroides, Thalassia hemprichii and Halophila ovalis. The average density per seagrass species in Orwer waters is higher (2101 ind/m2) compared to Ambroben waters (1553 ind/m2). The percentage of seagrass ecosystem cover in Orwer is higher (94.44%) than in Ambroben waters (91.53%). The characteristics of aquatic health indicators for seagrass ecosystems in Orwer and Ambroben waters show almost the same range of values, namely temperatures ranging from 29.47-29.97, salinity 33.27-33.97 oo/oo, and pH 7.57-8.46, the dissolved oxygen parameter shows different values between the two waters. Oxygen levels in Orwer waters are 10.47-14.37 mg / L, while Oxygen levels in Ambroben waters are 7.47-11.10 mg / L. Based on these results, it shows that both waters are still included in the category of healthy waters and meet the quality standard criteria for life requirements for seagrass ecosystems.