Sponges are major components of benthic marine ecosystems across the world. However, despite seagrasses being one of the key ecosystems in tropical environments, their associated sponge assemblages have been poorly studied. In this study we investigated seagrass and sponge assemblage composition in an Indo-Pacific seagrass meadow located surrounding Hoga Island in the Wakatobi National Park, South-east Sulawesi, Indonesia. We examined a continuous seagrass meadow, spatially separated into two sites, categorized into three zones based on the distance to the shore: high-shore, middle shore and near-reef-flat zones. We investigated the species richness, composition and abundance of both seagrass and sponge species across zones and sites. We found that the sponge assemblage composition was significantly different between sites and zones, while the seagrass assemblage was not. This suggests that the seagrass and sponge assemblages have different ecological drivers. Based on our observations, we propose that sponge adaptation to the prevailing environmental conditions in different seagrass zones may be reflected by sponge morphology. Furthermore, seagrass ecosystem management strategies should consider the different drivers of seagrass and sponge distribution patterns as they might be differentially affected by specific anthropogenic stressors.