Maerl beds, particularly those of Brittany, are important, structurally complex biogenic coastal habitats that form a unique ecosystem with high benthic biodiversity. Although they are relatively well studied throughout Europe, several faunal groups of maerl beds, such as those belonging to the meiofauna, have received little attention. We investigated the meiofaunal abundance, distribution and community structure, with a focus on nematode biomass and diversity, in a maerl area in the Bay of Brest, Brittany, compared with that on a sandy beach (Anse de Dinan, Brittany). Meiofauna was five times more abundant on the maerl bed than on the sandy beach, and 1.5 times more diversified (12 vs. 8 taxa, respectively). Nematode diversity was more than three times higher on the maerl bed than on the sandy beach and showed a distinctive nematode community that was absent from the sandy beach. Maerl beds create more heterogeneous microhabitats and promote a higher diversification of meiofauna and nematode communities than sandy beaches.