For a long time it has been discussed as to whether Melanelixia fuliginosa comprises one or two species: one darker, mainly saxicolous, and one lighter, mainly corticolous. To settle the question, a morphometric and a molecular analysis were carried out and analyzed using a principal component analysis (PCA). The morphometric analysis indicates a differentiation in several characters between material previously recognized as subspecies fuliginosa and glabratula, but also a considerable overlap in some of them. The molecular analysis of the nrITS DNA gene reveals a clear division of the taxa. Specimens belonging to Melanelia fuliginosa fall out in two different clades, which have good bootstrap support, corresponding to the subspecies fuliginosa and glabratula. Accordingly, we propose that the subspecies should be acknowledged as separate species, Melanelixia fuliginosa (Fr. ex Duby) O. Blanco et al. and Melanelixia glabratula (Lamy) Sandler & Arup.