In this study, more than 100 samples of Rhizocarpon in Xinjiang were used as materials to study the species diversity of Rhizocarpon in Xinjiang by morphological and anatomical observation, chemical composition analysis and molecular identification. The results obtained from this study are as follows: (1) seven species of Rhizocarpon distributed in Xinjiang were identified, including one newly recorded species named R. atroflavescens, and six common species, namely, R. badioatrum, R. disporum, R. geminatum, R. geographicum, R. grande and R. superficiale. (2) A subspecies search table for 22 kinds of Rhizocarpon in Xinjiang was compiled. (3) The phylogenetic analysis of Rhizocarpon in the genus Caryopsis showed that the results of molecular identification were consistent with those of morphological and anatomical characteristics, and the new recorded species in China was more clearly identified as pale yellow Caryopsis. (4) The regional distribution and elevation distribution of 22 species of Rhizocarpon in Xinjiang were analyzed. The results show that the 22 species of Rhizocarpon are distributed all over the world, with Asia being the most abundant. The 22 species of Rhizocarpon are distributed from low to high altitudes, but not distributed evenly, more species distributed in the high altitude range.