Abstract: Objects: The object of this paper was to determine the taxonomic status of a newly isolated of thermophilic microalga, and to study the stability of its phycocyanin to evaluate its possibility of application in food. Methods: The newly isolated algal strain was morphologically observed by optical microscope, and identified its taxonomic status based on its 16S rDNA sequence and the phylogenetic tree analysis. The phycocyanin of the alga was obtained by ultrasound-assisted extraction, and the stability of phycocyanin was investigated and evaluated based on the changes of the optical density measured with spectrophotometer under different levels of temperature, illumination and pH. Results: The alga cell was rod shape, straight or arc sometimes, binary fission, and was a branch of genus Thermosynechococcus. A crude extract of phycocyanin with a purity of 0.941 and a color value of 196.53 was obtained from the alga, and the yield was 11.37% (for dry mass weight). The stability tests showed that the phycocyanin was stable for 3.5 h at the temperature 60 ℃, its optical density retained 91.4% after illumination of 6000 lux for 7 d, the color was stable kept pH4.0~8.0 for 3.5 h, but it exhibited a poor stability in strong acid or strong alkali. Conclusion: The isolated microalga is a strain of the genus Thermosynechococcus. Its phycocyanin has good thermal-stability, photo-stability and acid-base-stability, exhibiting encouraging possibility for food application.