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Genetic studies have shown that the threatened crayfish Austropotamobius pallipes species complex is composed of two lineages (A. italicus and A. pallipes), both occurring in Italy. However, the issue surrounding their taxonomic status has not yet been solved even though the confused taxonomy may hamper attempts to conserve indigenous crayfish. The aim of this study was to develop methods for the morphometrical characterization of the A. pallipes species complex. Having analysed 18 morphometric variables on a total of 44 specimens of each lineage, we showed that the tip of the rostrum could be used to discriminate A. italicus and A. pallipes. Such discrimination was also obtained by analysing the size and shape of both the female spermatophoric plate and the male gonopods. These results confirm the potential to adopt morphometric studies to complement the genetic characterization of cryptic species.