A morphologically distinct population (var. almeriensis) of the lichen species Diploschistes ocellatus from southern Spain is examined using morphological and molecular methods. While the morphological examination revealed some unique features of var. almeriensis, the ITS sequence data did not support a distinction from D. ocellatus s. str. The Kishino-Hasegawa test did not rule out trees distinguishing between the two morphotypes, although spectral analytical data support an inclusion of var. almeriensis in D. ocellatus. The influence of potentially erronously aligned ambiguous sites is evaluated by analysis of different alignments. However, all alignments agree in placing all specimens of D. ocellatus together and, consequently, in the consensus tree D. ocellatus s. lat. forms a monophyletic clade with high bootstrap support.