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Individuals identified as Aricidea assimilis Tebble, 1959 were collected from ten localities across the Mediterranean Sea from 0.5 to 225 m depth in order to have a wide coverage of the species habitats and geographic range and to assess the effects of environmental factors and biogeographical barriers on molecular and morphological diversity. Two mitochondrial and one nuclear markers were used to reconstruct phylogenetic relationships and test the occurrence of cryptic species. We observed two highly divergent lineages, one including all individuals from shallow, sandy environments (<10 m depth) and the other with the individuals from deeper muddy bottoms (30–225 m depth). Less pronounced divergence was detected between morphologically distinct brackish-water individuals and the remaining shallow-water individuals. The divergence observed between deep-water and shallow-water lineages is consistent with the hypothesis of distinct species. The ambiguous results of species delimitation tests applied to the two shallow-water sub-lineages might instead suggest a process of incipient speciation, even if this hypothesis needs additional evidence. These results suggest that sediment represents the main factor driving genetic divergence and ultimately cryptic speciation in A. assimilis, while other depth-associated factors and geographical barriers do not seem to significantly contribute to the genetic architecture of this species, suggesting the occurrence of wide-range larval dispersal. [ABSTRACT FROM AUTHOR]