Pellia borealis Lorb. is a simple thalloid liverwort that originated after hybridization between two allopatric taxa: Pellia epiphylla N and Pellia epiphylla S. The morphological and anatomical similarity of Pellia species along with its plasticity cause difficulties in clearly defining the species. Species from the Pellia epiphylla complex differ from the remaining Pellia species by bisexuality. Microstructure of the gametophytes of all three taxa and sporophytes of P. borealis and P. epiphylla S was investigated using scanning electron microscopy. As a result of these observations, some new diagnostic characters between analyzed taxa were discovered. P. borealis shows a different pattern of papillae distribution on the dorsal surface of the thallus compared to ancestral taxa and has larger cells. P. epiphylla N was distinguished by the localization and shape of archegonia. Comparison of P. borealis and P. epiphylla S capsule surface showed a significantly different microstructure.