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 (Ar- throspira) 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 dif- ferent habitats and geographical isolation are the primary reasons for the above-mentioned result.