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Mnium cuspidatum Hedw. from the Bashuigou landscape of the Guandi Mountains, Shanxi Province, China, found to be associated with a cyanobacterium that was successfully isolated and cultivated under axenic conditions and designated as Microcoleus sp. GD based on its morphology. Phylogenetic analysis of 16S rRNA alone and of the 16S rRNA combined with the 16S-23S internal transcribed spacer (ITS) region, and the presence of an 11-bp insert in the 16S rRNA gene, indicated that Microcoleus sp. GD was as Microcoleus vaginatus. Phylogenetic analysis of the 16S rRNA gene sequences revealed that Microcoleus sp. GD formed a well-supported clade with aquatic epipelic strains of M. vaginatus from the Czech Republic and with desert strains from the USA. Microcoleus sp. GD was more closely related to the aquatic strains living at the seciment/water interface. The secondary structure of the 16S-23S ITS showed that the Box-B helix of Microcoleus sp. GD was structurally was similar to these strains but quite different from the desert strains. Furthermore, the D1-D1’ helices of all strains varied but Microcoleus sp. GD was again most similar to the aquatic strains.