Seagrasses are economically and ecologically important marine habitats. However, anthropogenic activities resulted in their decline globally. In the Philippines, MPAs were established, but most seagrasses need to be acknowledged and directly protected, thus affecting the ecosystem productivity. To prevent this scenario, baseline information that describes the status of seagrass beds is highly needed to help implement sound management practices. The present investigation was carried out to assess the effect of anthropogenic activities on the seagrass ecosystem in 15 municipalities as sampling areas across Southern Philippines. The study used focus group discussions, key informant interviews, and household interviews guided by structured questionnaires. Some 30 to 45 fishers and gleaners were interviewed in every municipality with 476 individuals. A matrix was developed for measuring anthropogenic activities complementary to random sampling of seagrass cover assessment. The anthropogenic activities considered to degrade the seagrass ecosystem and were analyzed in the matrix included tourism, gleaning/fishing, aquaculture, industrial and domestic activities. The result of the study showed that domestic, tourism and gleaning are the prevalent anthropogenic activities affecting seagrasses. The result further showed that higher anthropogenic activities affected lower seagrass percentage cover (R2=0.56). The result indicates that as anthropogenic activity increases, the cover condition of the seagrass ecosystem is averted. This implies that seagrasses should be acknowledged and included in the coastal management plans.