Two new species; Lobothallia crenulata Lun Wang & Y. Y. Zhang, L. lobulata Lun Wang & Y. Y. Zhang and one new variety; L. subdiffracta var. rimosa Lun Wang & Y. Y. Zhang, are reported from China and described, based on morphological, chemical and molecular characters. Phylogenetic analyses showed that these new taxa form monophyletic groups. Lobothallia crenulata and L. lobulata, together with L. hydrocharis, L. radiosa and L. recedens, form a well-supported clade, whereas L. subdiffracta var. rimosa is nested within the samples of L. subdiffracta. Lobothallia crenulata is characterised by its placodioid thallus, thickly pruinose upper surface with a rimose appearance, aspicilioid to lecanorine apothecia with a crenate thalline margin and concave, black and pruinose discs. Lobothallia lobulata is characterised by its placodioid thallus, pruinose upper surface with lobules, aspicilioid when immature, lecanorine to zeorine apothecia at maturity and concave to plane, dark brown, shiny and epruinose discs. Lobothallia subdiffracta var. rimosa is characterised by its areolate thallus, rimose and pruinose upper surface, lecanorine apothecia and slightly concave to plane, black and pruinose discs. Secondary metabolites were not detected in the two new species nor the new variety. A key is provided for the species of Lobothallia in China.