Ilyocypris Brady and Norman () is a widespread freshwater ostracod genus including about 30 living and 190 fossil species. The specific identification of the living Ilyocypris relies mainly on the appendages. An identification exclusively based on valves is rather complicated because of a high intraspecific variability of their characters in several species. This study aims to test the taxonomic significance of the valves characters through the examination of specimens unambiguously identified on the basis of their soft part morphology, in order to provide useful taxonomic criteria for the identification of Ilyocypris shells in fossil assemblages. Sixty‐five ilyocypridid specimens collected in mainland Italy and surrounding islands were analyzed. The patterns of valve surface ornamentation and of marginal ripplets were examined by electron microscopy. Moreover, the geometric morphometric analysis of the valve outlines was performed. Sixty‐two specimens could be easily accommodated in eight Ilyocypris species (I. bradyi, I. decipiens, I. getica, I. gibba, I. hartmanni, I. inermis, I. monstrifica, and I. salebrosa) according to the morphology of their appendages. Three additional specimens, with soft parts typical of Ilyocypris but clearly distinct valve morphology, were left in open nomenclature. Our results show that the outline analysis is often a valid tool to discriminate between different species. Conversely, valve ornamentation displays different degrees of intraspecific variability in some Ilyocypris species. The marginal ripplets are constant within each species population, but they do not always mirror the patterns reported by other authors; therefore, we do not consider them as reliable diagnostic character for specific determination. This study confirms that the identification of Ilyocypris species requires accurate description of appendages as well as external and internal carapace characteristics, and stresses the advantage of a combined neontological and paleontological investigation in solving taxonomic problems related to non‐marine ostracods.