The crenarchaeal diversity and phylogenesis of two hot springs in Tengchong were investigated and analyzed using the construction of 16S rRNA gene clone libraries. Total 18 crenarchaeal sequences were obtained and divided into 12 OTUs. The average similarities between the clone sequences from Wuming hot spring and Rebao hot spring and their closest sequences deposited in GenBank is 92.56% and 93%, respectively. Based on the phylogenetic tree constructed by using crenarchaeal 16S rRNA gene sequences, Wuming hot spring not only have hyperthethermophilic crenarchaeal clusters but also have the crenarchaeal clusters that have close phylogenetic relationship with non-thermophilic crenarchaeota. And most of the crenarchaeota in Rebao spring distribute in normal temperature groups. This study showed that crenarchaeal clusters in Tengchong hot springs have some differences with other hot springs in the world, and these springs represent two important environments for investigating the evolutionary origin of the non-thermophilic Crenarchaeoone library.