We present the first dataset of meiofauna associated with vermetid reefs (biogenic constructions of Mediterranean intertidal habitat) in two areas along the northern coast of Sicily, Italy. The vermetid reefs are characterized by a horizontal extension from the shore towards the open sea and can be divided into three zones (the inner margin, the cuvette zone and the outer margin) which differ in hydrodynamic features. We studied the spatial distribution of meiofauna along the horizontal axis of the vermetid reefs, investigating the communities inhabiting the sediment inside cuvettes (shallow pools inside the “cuvette zone”) located between the inner and the outer margins of the reefs. We observed an increase in meiofaunal abundance from the inner to the outer part of the reef (from 1808 ± 80 to 2992 ± 512 ind. 100 cm−2) in both areas. Moreover, we studied meiofaunal communities associated with the most abundant macroalgae (Cystoseira sp., Jania rubens, Palisada perforata, Dictyota sp. and Padina pavonica) living on the reefs, investigating the influence of habitat size (biomass) and identity (complexity) of macroalgae. We found that meiofauna varied in abundance (from 446 ± 51 to 1758 ± 231 ind. 100 cm−2 on P. perforata and Cystoseira sp., respectively), on different macroalgae, and that the habitat size significantly influenced these abundances, but its effect was dependent on macroalgal identity. In fact, we observed a positive correlation between meiofaunal abundance and algal complexity (fractal dimension). The high algal cover in the “cuvette zone” of the reefs could contribute to make this zone more suitable for meiofauna, in particular close to the outer margin where we found more complex macroalgae (i.e. Cystoseira sp.). These results confirm that vermetid reefs, with their structural complexity, may play an important role in structuring benthic fauna in intertidal habitats.