We introduce a new statistical method to select which morphological characters are most useful to identify monogenean species. The method estimates the average size overlap of candidate diagnostic structures among a set of species to individuate those that mostly differ between the species. To demonstrate our approach, we report a comprehensive analysis conducted on two of the most species-rich monogenean genera: Dactylogyrus Diesing, 1850 and Gyrodactylus von Nordmann, 1832. We demonstrate that, in contrast to common taxonomic practice, very few but highly diagnostic measurements are necessary to correctly identify a specimen. In particular, we found that most of Dactylogyrus and Gyrodactylus species can be classified on the basis of the width of the supplementary connecting bar and of the length of the hook sickle, respectively.