Thalloid liverworts with a complex anatomy and with star-shaped epidermal pores with strongly thickened radial walls in the surrounding cells have traditionally been accommodated within the Cleveaceae, which comprises three genera: Athalamia, Peltolepis and Sauteria. Based on phylogenetic inferences from three chloroplast genes (psbA, rpoC1 and rps4) sampled for 41 accessions, we tested the circumscription and the relationships of these genera, using six species of the Aytoniaceae as outgroups. Four main lineages are resolved, two corresponding to Peltolepis and Sauteria and two composing a polyphyletic Athalamia. The latter is here divided into Clevea and a narrowly defined Athalamia. The traditional definition of genera of Cleveaceae based on two characters (carpocephalum stalk position and anatomy) is rejected and morphological characters defining the genera are re-assessed. A revised generic delimitation is presented, including a key to the genera. Evolution of the genera of Cleveaceae is re-evaluated in the light of molecular results, and the misleading influence of homoplasy on past morphological classifications and phylogenies is discussed.