Phragmites australis is the dominant and constructive species among plant communities in the wetlands of the downstream of Yellow River, China. Its morphological characters were high variable in different habitats. Studies on Morphological and RAPD variation of 15 P. australis populations from this region showed that soil salinity was the dominant ecological factor that affected the morphological characters of P. australis. The basal diameter, height, leaf length, leaf width, internode length, internode accounts, panicle length were negatively related to salinity. 194 loci were amplified by RAPD, of which 9 loci was highly negative-related to salinity, and showed a tendency to prefer the habitats with fresh water. 4 loci were positively related to the salinity, and showed a tendency to prefer the salinized habitats. Most loci were neutral to salinity. The morphological and genetic characters of BZH were special, and the speciality should not be determined by salinity. The morphological characters were affected by genetic information and environment. The morphological characters should change gradually and continuously along environmental gradient under plasticity, but should changed continuously or not in genetic control. The relevancies among quantitive characters, ecological factors and genetic variation in natural populations still will still be a focus and difficulty of ecological genetics of P. australis in the future.