Macroinvertebrates are vital in coastal marine environments, with functions: ecological (e.g., food chain) and socio-economic (e.g., income generation for coastal gleaners). Different anthropogenic activities, including unregulated gleaning, pose potential threats to the assemblages of macroinvertebrates. However, studies related to assessing and comparing the community structures of macroinvertebrates in protected and exploited areas are poorly documented in the Philippines. Hence, this study aims to provide valuable information to formulate proper fisheries management, including the protection and conservation of macroinvertebrates and their supporting habitats. A fishery-independent and fishery-dependent surveys were conducted in three coastal barangays of Baganga, Davao Oriental, Philippines: one protected (control site) in Ban-ao and two exploited (gleaning grounds) in San Victor and Kinablangan to determine macroinvertebrate community structure and document local gleaning activities. Seventeen (17) macroinvertebrates were recorded, comprising nine (9) mollusks, three (3) crustaceans, and five (5) echinoderms. Four species (4) were abundant in the study sites: Dardanus sp., Monetaria annulus, Thalamita crenata, and Trochus maculatus. The community structure of macroinvertebrates in both exploited areas was influenced by gleaning of the coastal residents, resulting in lower species richness, density, and diversity compared to the protected area where collection was highly restricted. There is a need to ensure the sustainability of gleaning in these areas by providing protection on the existing macroinvertebrates in the area through a formulation of local subsistence fisheries management.