Reef systems are one of the most biodiverse and complex marine ecosystems. Invertebrate cryptic epifaunal communities (i.e, cryptofauna) associated with the epilithic algal matrix make up a large part of the reef biodiversity and play a critical role in their food webs. Yet, few studies have investigated the composition and abundance of the cryptofauna associated with EAM and the major drivers influencing patterns of community structure. Algae biomass, rates of predation, depth, and trapped particles (detritus and sediment) are among the main drivers of cryptofauna composition changes. In the South Western Atlantic, the epilithic algal matrix composes up to 70% of the benthic cover both in tropical (biogenic) and subtropical (non-biogenic) reefs, but information about the associated cryptofauna is limited. We sampled the epilithic algal matrix (EAM) of two sites in an equatorial Brazilian oceanic island, at three depth strata. In total, 106 operational taxonomic units (OTUs) belonging to 14 taxa were recorded (Foraminifera, Gastropoda, Bivalvia, Polyplacophora, Amphipoda, Tanaidacea, Cumacea, Ostracoda, Decapoda, Polychaeta, Cnidaria, Sipuncula, Echinodermata and Chironomidae). Gastropods were the most diverse group (48 OTUs) and second most abundant (n = 1585). Total invertebrate abundance and composition, as well as abundance of each taxa, were influenced by EAM characteristics (algae biomass and coarse particulates) and depth. Foraminifera abundance increased as algae biomass increased, due to the presence of Large Benthic Foraminifera (LBF) which may associate with algae for sunlight protection. Mollusks were mainly represented by the detritivorous Barleeia rubrooperculata. Richness of taxa in EAM observed here was similar to values observed in frondose macroalgae elsewhere despite the low taxonomic resolution applied, indicating its potential as a cryptofauna biodiversity reservoir.