Rhinolophus yunnanensis was published in 1872 by Dobson on the basis of two male and one female specimens collected in Hotha, China (1371.6m above sea level), and later merged into R. pearsonii by himself. Andersen (1905) compared the description and diagram of the species and pearsonii and found that they should belong to two separate species. Corbet & Hill (1992) also suggested that it should be restored as a separate species, R. yunanensis. Wu et al. (2009) believed that this species was established based on the samples and karyotypes of Emei Mountain in Sichuan, China (2n=46, and <pearsonii> karyotype 2n=44).
Rhinolophus yunnanensis is endemic to China and is only distributed in western Yunnan.
Has been included in the China Biodiversity Red List - Vertebrate volume, assessment level: vulnerable VU.