This study investigates how anatomical characters can be used to differentiate two morphologically close species, Melanohalea olivacea (L.) O. Blanco et al. and M. septentrionalis (Lynge) O. Blanco et al. Although the two species are morphologically differentiated, mainly based on the position and shape of pseudocyphellae on the lobes, poorly-developed specimens can be difficult to identify based on morphology alone. For example, in Switzerland, both species are at the south-west limit of their distribution range and most specimens are small and not fully developed. In such cases, anatomical characters are particularly useful in separating the two species. Five anatomical characters were studied: spore length and width; hymenium, subhymenium and hypothecium height. A nested ANOVA showed that variation of spore length was 155 times greater between species than between individuals of the same species, itself 5 times higher than within individuals. In a Principal Component Analysis, despite a substantial variation of the anatomical characters within both species, a significant species differentiation appeared distinctly on the first axis (P < 0·001), which accounted for 62·35% of the total variance, and the type specimens nested within each species. Finally, a Discriminant Linear Analysis assigned 100% of the individuals to their species class, the best predictors to discriminate between the two species being subhymenium height and spore length. These characters proved to be powerful in identifying specimens with a poorly-developed morphology and confirmed the presence of M. olivacea in Switzerland.