The burrowing brittle-star Acrocnida brachiata has so far been regarded as a single, easily identifiable species. Recent studies showed habitat-related differences in maximum size, life span, breeding time and recruitment between intertidal and subtidal populations, which at first were attributed to environmental effects on individuals within the same species. Molecular data, however, strongly suggested the existence of two distinct lineages and ultimately two cryptic species with clear bathymetric segregation. Morphological evidence had so far not been presented, because any differences were interpreted as intraspecific variation. We collected A. brachiata from intertidal and subtidal habitats at the coast of Brittany, France, and examined 15 specimens of each group externally by SEM. A key character of A. brachiata is that the scales at the edge of the disc and on the ventral side are conically enlarged. Intertidal individuals showed a sparser disc scalation, more spine-like than conical ventral disc scales and spatulate, distally widened arm spines. In addition, we dissected several specimens of different size and examined the internal skeleton by SEM. The oral plates showed a rib-like structure on their abradial face that differs between individuals from either habitat. Subtidal specimens have fewer ribs than intertidal ones. These consistent differences support the existence of two species within A. brachiata. To describe the second species, we needed to establish the identity of A. brachiata. We describe a neotype, because no type material has been preserved since it was first described; it corresponds mainly to subtidal samples. The new species is described as Acrocnida spatulispina sp. nov. The taxonomic status of Acrocnida has been debated over the years with reference to its close affinities with Amphiura chiajei. We compared the species of Acrocnida with A. chiajei and Amphiura filiformis and found that Acrocnida is indeed morphologically similar to A. chiajei, among other characters by a similar oral plate structure, whereas A. filiformis differs greatly from Acrocnida as well as A. chiajei. Most strikingly, it has a different type of oral plate. These findings indicate that fundamental taxonomic changes may need to be made in the family Amphiuridae in the future.