For over a century, species delimitation was a critical task for biologists, concerning both species concept and operational methods necessary for the individuation of taxa boundaries. According to the recent approach of integrative taxonomy, species have to be considered as hypotheses that should be tested with different methods. Ecological interchangeability can be an element that can corroborate the separation of two putative taxa, but ecological data are often difficult to use. Ecological Niche Models (ENMs) provide a quantification of niche parameters and could be a useful tool for investigating taxa boundaries. For this purpose, we used ENMs for testing ecological (climatic) differentiation in three pairs of related taxa recently subdued to taxonomical revisions without explicitly considering ecological evidences. The selected taxa pairs are: Rhaponticum bicknellii (Briq.) Banfi, Galasso & Soldano and R. heleniifolium Godr. & Gren.; Gentiana burseri subsp. actinocalyx Polidori and Gentiana burseri subsp. villarsii (Griseb.) Rouy Fritillaria tubaeformis Gren. & Godr. subsp. moggridgei (Baker) Rix and Fritillaria tubaeformis subsp. tubaeformis. For each pair, we assessed niche overlap, niche equivalency and niche similarity in both multidimensional environmental space (E-space) and geographical space (G-space).