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Aim Riparian ecosystems are regarded as vulnerable to the effects of climate change. Because of their reliance on passive dispersal to migrate from areas where conditions have become unfavourable, plants are particularly susceptible. On dryland river floodplains, the species diversity of herbaceous annuals is often high while that of structurally dominant woody perennials is low. We examined gene flow genetic structure and dispersal in Acacia stenophylla, a small perennial tree widely distributed throughout river systems of inland Australia. The role of the river corridor in shaping patterns of gene flow and genetic structure is also investigated. Location Murray-Darling Basin, south eastern Australia Methods A total of 127 individuals, from 12 subpopulations located on seven rivers were genotyped at 13 microsatellite loci. Several population and landscape genetic tools were applied to the microsatellite data to evaluate spatial patterns of gene flow and genetic structure and make inferences regarding possible modes of dispersal. Results High gene flow and weak genetic structure was identified for the 12 subpopulations of A. stenophylla sampled, a surprising result given large distances between subpopulations. Pairwise genetic distance between subpopulations was low to moderate and could largely be explained (R-2 = 0.68) by two variables: distance along the river and the proportion of no flow days. structure analysis revealed two genetic clusters. Subpopulations located on the Darling and Lower Balonne rivers were dominated by cluster one while subpopulations from the Warrego and Paroo rivers showed largely mixed ancestry with individuals descending from both clusters one and two. Main Conclusions These results indicate that the river corridor facilitates extensive gene flow between subpopulations of A. stenophylla in this system. Hydrochory appears to be the dominant process; however, upstream movements of propagules most probably via animal movement are sufficient to negate effects expected under unidirectional dispersal.