Ecologically important marine ecosystems should be identified and protected, as is the case of the poorly known SW Atlantic rhodolith beds. Understanding the main variables predicting biodiversity patterns is essential for determining priority areas for conservation. Here, we analyzed the macroinvertebrate associated with rhodoliths from euphotic and mesophotic zones from the Fernando de Noronha Archipelago investigating the drivers of diversity distribution in this habitat. Rhodoliths were sampled and vagile macroinvertebrates (>500 m) were classified and quantified. We verified that estimated density of organisms associated with rhodoliths in the euphotic zone was 17 % greater than the mesophotic zone. The communities along depth zones show dissimilarities, suggesting that both environments are ecologically distinct. Comparisons with other ecosystems revealed that rhodolith beds have similar diversity of macroinvertebrates. We also found that four of the six tested variables predicted 85% of the variability observed in the vagile macroinvertebrate community (i.e. average diameter, depth, biomass of macroalgae and density of rhodoliths in the bed). These variables should be taken into account in future research in modeling the biodiversity associated with the rhodolith beds. This is especially relevant in the SW Atlantic where the rhodolith beds seem to harbor an associated biodiversity greater than previous works had indicated, moreover, they represent one of the main ecosystems that are often superimposed with mining activities.