Investigating plant genetic diversity can provide basic knowledge for vegetation conservation and ecological restoration. Leaves of 280 individuals from seven Phragmites australis populations in the Yellow River Delta were sampled. We analyzed the genetic structure and diversity of seven P. australis populations at 12 loci using microsatellite markers,and analyzed the relationship between genetic diversity and salinity. Results showed that the genetic diversity in these P. australis populations was low. The Nei's genetic diversity index (H) ranged from 0.077 to 0.107 and the Shannon information index (I) ranged from 0.133 to 0.185. However,the genetic diversity of two populations from high marsh was relatively high (H= 0.101-0.107,I = 0.176-0.185) . The genetic divergence of these populations was low (GST = 0.062) ,with most of them coming from intra-population. Moreover,there was no significant relationship between genetic distance and geographic distance (r = 0.026,P = 0.354) . However,the relationship of genetic diversity and salinity was positively significant (R_(adj)~2 = 0.597,P = 0.026) . These results suggested that P. australis populations from tidal marsh in the Yellow River Delta should be protected and that seedlings or propagules from populations of other regions could be used to enrich genetic diversity of P. australis in the degraded wetland during restoration
