Four groups of algas, isolated from the Taklimakan desert, were identified by morphological characters in this study. The pH effect of the growth of algae is analyzed according to the growth curve, and the phylogenetic tree was pictured. It shows that the group a belongs to the oval algae, and group b, c and d belong to the spherical algae. The optimum suitable pH values for the group a desert algae was 6.0, 8.0 for the group b and d; the same value of original BG-11 for the group c. Four representative strains of desert algae gene sequences were identified by using the 18S rDNA sequence analysis method. It shows that the strain of 3YS16① (group a) and the strain of 3YS21-1 (group c) have close genetic relationship with the Chlamydomonas incerta; the strain of KXII(2) (group b) has close genetic relationship with the Chlorosarcinopsis bastropiensi; the Strain of YS2-3 (group d) has close genetic relationship with Chlorosarcinopsis communis. This study determined the classification status of four groups of algae and the optimal pH growth conditions, and provided theoretical basis to the molecular biology studies of desert algae and applications in food industry.