Pigment and fatty acid profiling reveal differences in epiphytic microphytes among tropical Thalassodendron ciliatum meadows

•Variation in the host dynamics can have potential consequences on the abundance and composition of epiphytic microphytes.•Meadows with high leaf turnover exhibited low epiphytic microphyte biomass due to the effect on leaf retention thus low microphyte colonization.•Epiphytic diatoms are sensitive to changing host characteristics such as seagrass leaf surface area. Tropical seagrasses support abundant and diverse epiphytic microalgae that form the base of seagrass food webs. To help better understand the influence of structural variability of tropical seagrass meadows on associated microalgal epiphytes, we quantified the relative abundance and distribution of epiphytic microphytes in subtidal meadows of Thalassodendron ciliatum with varying seagrass canopy structure, using pigments and fatty acid (FA) profiling. We observed significant differences in microalgal epiphytic communities (diatoms and Rhodophyta) among four seagrass meadows, which was best explained by seagrass leaf surface area. Contrary to expectations, seagrass meadows with lower leaf surface area supported higher relative epiphytic microphyte abundance than those with higher leaf surface area. These results increase understanding of how spatial variability of structural components in seagrass meadows can influence their functional components, with implications on the availability to primary consumers.