Abstract In the present paper, the brackish-water mudsnail genus Hydrobia is used to assess the degree of anatomical differentiation among cryptic species. Detailed anatomical data for seven populations from four taxa are compared to genetic data in order to test whether there are discrete anatomical differences among taxa, whether it is possible to partition the total anatomical variation into hierarchical among-taxa and among-population components, to find those anatomical characters that statistically discriminate taxa, and to make inferences about the mode of evolution. A qualitative anatomical analysis did not yield any character states that could be used to differentiate among taxa, and a PCA of quantitative anatomical characters did not discriminate among species. Moreover, no significant variance component could be detected in the nested analysis of morphological variance among lineages and/or populations. However, discriminant analyses (DA) with mtDNA lineages as grouping variables resulted in highly significant discrimination models for sexes combined, females and males. The DA's retained up to 16 variables and up to six of them showed significant differences among lineages. Generally, shell characters were performing better than soft body characters. The poor performance of soft body characters is attributed to an unusually high intraspecific variability in Hydrobia. Anatomical, ecological, and biogeographical characteristics that could have contributed to the high variability are discussed. The evolution of anatomical variables among lineages was tested for deviation from expectations derived from a stochastic evolution model. The test showed that the null hypothesis of stochastic evolution according to the Brownian motion model could not be rejected, indicating that anatomical characters in Hydrobia are neither subject to diversifying nor to constrained evolution. Based on genetic and supportive anatomical data, one of the taxa in the study, Hydrobia sp. A, is considered to be a new species and formally described as Hydrobia djerbaensis n.sp. Species nova: Hydrobia djerbaensis Wilke, Pfenninger & Davis.