Rivers favour gene flow by hydrochory and habitat connectivity, and bring heterogeneous selection pressures on genotypes. River regulations (e.g. dams) could influence the hydrologic conditions and then change the effects of rivers on genetic diversity of riverine plants. In Ningxia Plain of China, we investigated the intraspecific variation of Phragmites australis using nine plant functional traits, eleven nuclear microsatellites and two chloroplast DNA fragments. Along the Yellow River for approximately 390 km in Ningxia Plain, we collected P. australis from eleven sampling sites upstream of Qingtongxia Dams and eleven sites downstream. We also added eight sites far from the watercourse in the northwest of Ningxia Plain as the non-riverine population. The downstream population had a higher genetic diversity than the upstream population, but a lower haplotype richness. The downstream population had a weaker genetic differentiation with the upstream population (Fst = 15.98) than with the non-riverine population (Fst = 27.76). The same genotype occurred mostly within sites, but two occurred in several sites along the Yellow River. In the individual level, the pattern of isolation by geographical distance was most significant in the non-riverine population, and there was a significant correlation between functional and genetic variation in the non-riverine and upstream populations but not in the downstream. Our findings provide empirical evidence for the significant role of river corridor in propagule dispersal and genetic diversity, and highlight the potential negative effects of dams on genetic connectivity and local adaptation of riverine plants.