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The understanding of macroalgae functions and processes requires a good understanding of the spatial distribution of the functional diversity of macroalgae. In coral reef environments, this information remains fragmentary. Here, based on 314 species sorted according to a set of 10 functional traits, the functional niches of macroalgae at three remote coral reefs of the iles Eparses in the Indian Ocean (Europa, Glorioso, and Juan de Nova) are described. For the comparison of intra- and inter-reef functional structures, we characterized both taxonomic and functional beta diversities, and their turnover and nestedness-resultant components. Within the three reefs, we observed strong taxonomic and functional dissimilarities across sampling sites, mainly determined by turnover. Null models highlighted several processes, which structured macroalgal assemblages across sites: a combined effect of environmental variables (geomorphology and wave exposure), limiting similarity and stochastic effects. At the inter-reef scale, the three reefs only shared a small number of species, but the functional beta diversity between Glorioso and Juan de Nova was weak. This suggested that although assemblages were different, fairly similar environmental conditions may have homogenized macroalgae functions through both ecological and evolutionary scale processes. Our results support the idea that macroalgal assemblages can provide similar functional trait portfolios, despite distinct species composition. We stress the need to focus on macroalgae life-history traits for a better understanding of the processes structuring their communities.