Specimens obtained from ten populations of a Monacha species from the central Apennines were compared with six molecular lineages of Monacha cantiana s. l. (CAN-1, CAN-2, CAN-3, CAN-4, CAN-5, CAN-6) and two other Monacha species (M. cartusiana and M. parumcincta), treated as outgroup, by molecular (nucleotide sequences of two mitochondrial COI and 16S rDNA as well as two nuclear ITS2 and H3 gene fragments) and morphological (shell and genital anatomy) analysis. The results strongly suggest that these populations represent a separate species for which two names are available: the older Helix pantanellii De Stefani, 1879 and the junior M. ruffoi Giusti, 1973. The nucleotide sequences created well separated clades on each phylogenetic tree. Genital anatomy included several distinctive features concerning vaginal appendix, penis, penial papilla and flagellum; instead, shell characters only enabled them to be distinguished from M. cartusiana and M. parumcincta. Remarkably, populations of M. pantanellii show high morphological variability. Shell variability mainly concerns size, some populations having very small dimensions. Genital variability shows a more intricate pattern of all anatomical parts, being higher as regards the vagina and vaginal appendix. Despite this morphological variability, the K2P distance range of COI sequences between populations is narrow (0.2–4.5%), if we consider all but three of the 53 sequences obtained. This research confirmed that the species of Monacha and their molecularly distinguished lineages can only occasionally be recognised morphologically and that they have significant inter- and intra-population variability. The possibility of using an overall approach, including shell, genital and molecular evidence, was taken in order to establish a reliable taxonomic setting.