Rhizocarpon smaragdulum Davydov & Yakovchenko sp. nov. is described and a phylogenetic analysis (ITS, mtSSU) is presented, confirming its distinctiveness and indicating a sister relationship with R. suomiense and R. subgeminatum. The species is unique among yellow Rhizocarpon species in having a single hyaline ascospore per ascus. The phylogenetic tree suggests that the number of ascospores per ascus has been reduced in Rhizocarpon more than once during the course of its evolution. Two new distributional records are also reported: Rhizocarpon atroflavescens is new for Siberia and R. norvegicum is new for the Altai Mountains. Rhizocarpon norvegicum in this region grows on rocks and is also lichenicolous on Acarospora bullata.