Abstract Dianthus virgineus encompasses a very complex taxonomic group (traditionally called D. sylvestris group) including an array of units of doubtful taxonomic rank and value. Recent work identified three genetic lineages within this complex that showed strong genetic isolation, and clear geographical boundaries (i.e., “Alpine”, “Balkan”, and “Apennine” lineages). We evaluated the contribution of 33 morphological characters in differentiating such genetic units, by also investigating the effect of geographical and ecological drivers on the characters showing major discriminating power. The morphological measures were taken from a large number of populations (N = 97) included in the sample used for detecting the three genetic lineages. Our work reveals that these lineages can be morphologically discriminated by a series of character‐states that are traditionally considered of relevant taxonomical value. We also inferred a significant geographical and ecological effect on most characters, which varied gradually with latitude, longitude, and mean annual temperature. Overall, our data suggest that the three biological units can be referred to D. inodorus (L.) Gaertn. (“Alpine” lineage), D. sylvestris Wulfen (“Balkan” lineage), and D. virgineus L. s.str. (“Apennine” lineage). We also provide an identification key to discriminate these three taxa.