The samples of Spirulina (Arthrospira) platensis from different habitats were analyzed by the RAPD. The result shows that there are obvious differences in the molecular level between the Spirulina (Arthrospira) platensis from alkaline lakes in Erdos Plateau and the one from Chad Lake, and the homology of DNA in the amplified polymorphism of the Spirulina (Arthrospira) platensis only reaches 48.23%. The different habitats and geographical isolation are the primary reasons for the above-mentioned result.