Although the arid and subarid lands cover one third area in China, yet the soil blue-green algae flora and its community of desert area has not been reported previously. In this paper, the preliminary study on the species composition and abundance of the blue-green algae community of the sanddunes, gobis and hills the some places in the east and middle parts of the Qaidam Basin is reported. 21 species of blue-green algae were identified. Among them Phormidium foveolarum and Lyngbya digueti occurred most frequently, then Microcoleus vaginatus and Schizothrix undulatus. Myxosarcina chrococcoides, M. concinna, Schizothrix undulatus, Tolypothrix fragilis, Anabaena variabilis f. tenuis and A. oscillatorioides f. minor were new records for China. The relationship between the environment and the blue-green algal distribution was determined and analyzed using the methods of fuzzy cluster, cluster and multivariate linear correlation. It is concluded that the moisture of air and soil plays the primary role in the growth of soil algae in desert area. The species number and abundance of soil algae in Qaidam Basin are affected by soil ionic strength and soil texture relating to the cohesiveness and retention of water. Significant positive correlation between biomass and PO43--P contents in the soil was also found.