Macrobenthos, including mollusks, are the key players in seagrass beds. This study aimed to determine the community structure of bivalves and gastropods associated with the seagrass beds in IBMS, such as the frequency of occurrence, ecological indices, and canonical correspondence analysis between these parameters and the mollusks. Sampling sites are at Alubijod White Sand Public Beach (Site 1) and Villa Igang Beach Resort (Site 2). A 60 m measuring tape was used to lay 50 m transects, 50 m apart, perpendicular to the shoreline for each seagrass bed site. Seven transects with sample quadrats at 5 m, 25 m, and 45 m marks using a 0.5 m x 0.5 m stainless steel quadrat were conducted for Site 1 and six transects for Site 2. The coordinates and the parameters were measured in-situ. Sampling was conducted at negative low tide. 38 genera were recorded in one Mytilidae family and unknown bivalves and gastropods, while 16 genera and one family are common to both sites. Of these, 16 genera and one family are common to both sites. Furthermore, 26 bivalves and 32 gastropods for 58 individuals were found in Site 1, while 165 bivalves and 29 gastropods for a total of 194 individuals in Site 2. Nevertheless, the frequency of bivalves and gastropods is comparatively the same regardless of the site in IBMS. On the other hand, the sites within and outside the IBMS had a marginal difference in diversity, evenness, and population density. Moreover, the parameters and the benthic composition were not found to influence the community structure of mollusks. Further research needs to be conducted to determine which anthropogenic factors negatively affect the bivalves and gastropods on the seagrass beds in IBMS.