Species identification on the basis of specific mass profiles of peptides and small proteins – proteomic fingerprinting – is becoming increasingly popular among zoologists. While the method has been successfully applied to various groups of invertebrates, its applicability to gastropod species has not yet been tested. Here we use the cryptic brackish water mudsnail genus Ecrobia as a model taxon to assess the discriminative power of this approach in comparison to DNA-based approaches. Our pilot study shows that proteomic fingerprinting discriminates most species of Ecrobia well and that the discriminatory performance is similar to that of molecular phylogenetics based on mitochondrial genes. Thus, Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) may serve as a relatively inexpensive tool for an efficient identification of gastropod species.