It is still unclear whether variation in nature is discrete or continuous. Species are commonly regarded as discrete units, occupying distinct ecological niches. With the wide availability of molecular methods, species are now often recognized genetically rather than morphologically, as is, for example, the case for the more than 40 genetic species of the ostracod Eucypris virens (Jurine, 1820). Here, we used B-spline outline analyses of the right valve in an attempt to morphologically recognize the genetic E. virens species from Europe, North Africa, and Australia from their valve shape. Ostracod outline analyses capture valve variability in a multidimensional and quantitative way and allow fast screening of large numbers of specimens. In our study, two significant valve clusters were identified from subsequent ordination and regression analyses but without any clear link to genetic species identity, geographical location, gender, or reproductive mode, whether standardized for size or not. There is also no effect of polyploidy on valve shape. Thus, genetic E. virens species cannot currently be recognized morphologically by valve shape and are considered to be cryptic species. Because of their extensive fossil record, ostracods are widely used as proxies for palaeoecological applications such as reconstructions of past climates. Species within fossil ostracod assemblages can usually be identified only by their valve characters. Our results imply that the occurrence of cryptic species complexes leads to underestimates of fossil diversity in palaeontological studies. It is further possible that these cryptic species have different ecological tolerances, with the risk of weakening predictions based on palaeoecological reconstructions. Therefore, genetic studies should be mandatory for defining effective conservation units and studying ecological reaction norms of cryptic ostracod and other animal and plant species.