Seagrass-associated epifaunal macroinvertebrates communities are complex ecosystems patterned with diel shift rhythms and niche cycles. Most studies focus on diurnal rhythms as researchers engage in daytime collections, creating community structure frameworks accustomed to this analysis. Less is known to nocturnal cycles and diurnal-nocturnal shifts as community structure in these periods may offer a holistic ecosystems framework rather than a diurnal outlook. Moreso, literature is limited in lunar-influenced community structure in seagrass-associated epifaunal macroinvertebrates. This paper seeks to identify the community structure patterned on lunar illumination percentages based on waning gibbous, full moon, waxing gibbous, waxing crescent, and; waning crescent. Each phase differs in illumination percentage, and identifying community structure may depict activity and favorable adaptive mechanisms among the community. Four stations were established in Eastern Samar, Philippines, in a month-long collection, laying 50 meter transect lines with five quadrats placed every 10 meters in shallow waters covering seagrass beds. Results show that mollusks dominated the structure together with diverse echinoderms, arthropods, poriferans, and annelids. During the full moon, the species’ relative abundance was the highest value compared to other lunar phases. This structure was followed by waning gibbous, waxing gibbous, waxing crescent, and; waning crescent. In reference to the illumination percentage, community structure was influenced in favour for a brighter lunar phase based on the computed relative abundance. As lunar illumination percentage was reduced, assemblages of epifaunal macroinvertebrates were also reduced. This community structure indicated assemblages in response to lunar illumination, lunar phases, and the framework of the seagrass ecosystems should be monitored using this outlook.