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In this paper, we study in Rhizocarpon Ramond ex DC. species by the method of combining phenotypic characteristics (morphology, anatomy and chemistry) with genotypic characteristics (ITS sequence). The aims of this present paper are to clarify the status of some species and explore the relationship between phenotype and genotype in Rhizocarpon. During the study on Rhizocarpon species from southwest China, R. sichuanense Y. M. Zhang, L. Hu & W. C. Wang sp. nov. is described as a new species in this genus. The new species is morphologically similar to R. cinereonigrum Vain and R. sinense Zahlbr., which also produces brown thallus, medulla I-, 8-spored ascus and brown ascospores with 1-septa. But it can be distinguished by the scattered, areolate to subsquamulose thallus, a distinct black prothallus, large ascospores are [(27-)32-42.5] μm × [12.5-17.5(-20)] μm and the presence of barbatic acid is in the thallus. In phylogenetic trees, it is also similar to R. badioatrum (Flörke ex Spreng. ) Th. Fr. which can be distinguished by the more continuous thallus with diffractaic acid or without secondary products, and the smaller spores [(23-36) μm ×(13-16) μm] than this new species. The phylogenic results are as follows: (1) The new species R. sichuanense belongs to badioatrum group which belongs to Rhizocarpon subg. Phaeothallus; (2) It is unsuitable to classify some groups only based on anatomical characteristics (spore size and separation type) in Rhizocarpon, the chemical characteristics should also be considered. In this paper, the achievement of ITS sequences provide the basic data for an establishment of a more reasonable and natural classification system. In addition, we provide high resolution pictures of morphological, anatomical and chemical characteristics as well as detailed descriptions of the new species. The key to the species of Rhizocarpon subg. Phaeothallus with 1-septa brown spore (Badioatrum group) in the world is also provided, which will provide basic data for the further studies in this group. [ABSTRACT FROM AUTHOR]