Molecular diversity of halophilic archaea from Ayakekumu Lake was investigated by the polymerase chain reaction (PCR) amplification and culture methods. Ayakekumu Lake located in Altun Mountain in Xinjiang in high altitude (approximately 3880 m) with a slightly alkaline pH (7.9). Low temperature, abundant sunlight, low nutrient levels, high wind speed, and remote geographical location made Ayakekumu Lake become an ideal ecosystem to examine the biological diversity in a stress environment. Unfortunately, Ayakekumu Lake has not been systemically investigated because of the difficulty to get access to the area. 19 water samples and 15 soil samples were taken from 19 sites within Ayakekumu Lake in a field trip on December 2003 and March 2004. The cultivation of microbe used five different media. Under aerobic culture conditions, total 186 halophilic microorganisms, including halophilic archaea, moderately halophilic bacteria, and halotolerant bacteria were isolated. The 16S rRNA gene sequences of 62 red strains were amplified using PCR, determined by DNA sequencer and analyzed thought BLASTn program subsequently. Results revealed that all sequences belonged to six genera grouped within the Halobacteriaceae. Mostly 16S rRNA gene sequences related to the genera Halorubrum (47%) and Natrinema (24%) were detected. The observed microdiversity reflected the conditions of the habitat, which select for better adapted microbes. Haloarchaeal strains were assigned to operational taxonomic units (OTUs) based on sequence analysis. Subsequent analysis using Shannon index indicated that cultured halophilic archaeal diversities are not significantly different between winter samplings and spring’s in Ayakekumu Lake. Similarity values of haloarchaeal 16S rRNA gene sequences to known sequences were less than 97%, suggesting the presence of two novel taxa. In addition, taxonomic characteristics of Natrinema altunense and Halobiforma lacisalsi isolated from Ayakekumu Lake have been described previously. The discovery of novel species provides new opportunity to further examine the diversity of these halophilic microorganisms in Ayakekumu Lake.