Abstract: The genetic differences among different reed ecotypes was analysed on four ecotypes of reed (Phragmites communis) in Linze County, Gansu Province, using RAPDs and allozyme genetic diversity analysis. Ten base random primers were used in the RAPD analysis and 16 primers were chosen on the basis of repeatedly forming significant polymorphism products. Of a total of 559 amplification bands 489 (87.5%) were polymorphic. Using 12 allozyme loci, allozyme genetic diversity analysis, showed there were nine gene sites with polymorphisms. The average percentage of polymorphic sites was 34.1%. The Results indicated that notable molecular genetic diversity and different ecotype reed allozyme expression divesity existed among the different ecotypes but genetic diversity between individuals of the same ecotype was slight. This is consistent with the distinct differences between the habitats and together with the morphological and physiological variations, it demonstrates that these differences are involved in different reed ecotype genetic differentiation.