Natural selection can lead to speciation, but its effects depend on amount of morphological variation within populations. In Ostracoda, the appendages enclosed within the calcified carapace are less influenced by environmental conditions in comparison with carapace valves. Here, we explored morphological variation of appendages and labrum in cosmopolitan genus Heterocypris, investigating the species occurring in Europe. With the aim to overcome taxonomical problems, both traditional and geometric morphometrics were applied. The relative lengths were analysed by one-way ANOVA and post-hoc tests to determine interspecific variation and sexual dimorphism. Significant traits were further analysed by Canonical Variate Analysis separately for males and females as segment width/length ratios and relative length of claws and setae ratios. Landmark-based geometric morphometrics were applied to analyse shape variation of the labrum and traits of the maxillular palp. From this, a new perspective on morphological variation within this genus emerged. Relative measurements of the second segment of the maxillular palp, and relative lengths of the natatory setae were found to be the characters that contribute most to discrimination among Heterocypris species. The most important discriminant traits in females are the relative lengths of the G2 and G1 claws. Heterocypris exigua is additionally described, as all findings demonstrated that this is the most distinctive species, the most similar to H. gevgelica. In conclusion, we found that in comparison with maxillular palp and other analysed characters, labrum traits showed as more reliable and deserve more attention in descriptions of new species.