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Foundation species traits that structure communities are rarely experimentally examined; thus, a predictive understanding of their functions lags behind patterns of observed species associations. Red mangrove Rhizophora mangle roots form complex living habitats that support diverse epibiont communities, making them a model system for testing links between variation in foundation species traits and associated biodiversity. Here, we compared epibiont community composition between living and non-living mangrove roots, as well as root mimics, to test how foundation species traits affect community structure. We also quantified the community structure of associated mobile invertebrates to examine their relationship with secondary foundation species (e.g. sponges, bivalves) that grow on the roots. After 14 mo of colonization and succession, substrate composition (i.e. mangrove, wood, PVC) had significant effects on community composition, richness, and abundance of sessile epibionts and mobile invertebrates. Non-living mangrove roots were 5 times more likely to deteriorate, and consequently had the lowest epibiont richness and abundance. We found strong positive relationships between mobile invertebrate richness and the abundance, measured as biomass, and richness of sponges and bivalves, suggesting that variation among roots in secondary foundation species play an important role in mediating mobile invertebrate community composition. This study highlights the functional role of habitat structure and how rapidly that function can be lost without biogenic maintenance. Our results indicate the importance of facilitation cascades in fostering diverse mobile invertebrate communities and highlight both advantages and limitations in using artificial structures in restoration programs.