Morphology of both the valves and limbs of several parthenogenetic populations of the widespread non-marine ostracod Cryptocandona vavrai Kaufmann (sensu lato) living in groundwater habitats of western (France) and south-eastern Europe (Romania) was examined for the extent of intra- and interpopulational variation. Geometric morphometrics and multivariate statistics were employed for the description of the valve morphological disparity whereas the discriminant analysis was performed for the comparative analysis of the limb chaetotaxy. The ranges of the most studied limb traits principally overlapped among the populations, however considerable differences in the carapace shape and size, reflecting microevolutionary changes at a macro-scale (inter-population) level, allowed distinguishing quantitatively some Romanian populations which deserve a separate specific status. Hence, a new species Cryptocandona racovitzai sp. nov. is described which differs from C. vavrai sensu stricto mainly in larger size, in more triangular valve shape as seen laterally and in less developed inner lamella of the valves. Finally, after examination of more material from Romanian groundwaters, we hypothesised the presence of more new species within the studied lineage and concluded that Cryptocandona vavrai sensu lato is a polymorphic lineage consisting of several geographically differentiated species rather than just only one widely dispersed species.