Gene-flow is a key evolutionary driver of spatial genetic structure. Spatial patterns in genetic structure reflect demographic processes and dispersal mechanisms. Thus, understanding how genetic structure is maintained across a landscape can assist in setting conservation priorities. In Australia, floodplains naturally experience a highly variable flooding regime, which structures the vegetation communities. Temporal variability in flooding, and spatial variability in topography, means communities on floodplains are often spatially and temporally discrete. Flooding plays an important role, connecting communities on floodplains, through enabling dispersal via hydrochory. Water resource development has changed the lateral-connectivity of floodplain-river systems. One possible consequence of these changes is the reduced physical and subsequent genetic connections. This study aims to identify and compare the population structure and dispersal patterns of lignum (Duma florulenta) and river cooba (Acacia stenophylla), across a large inland floodplain using a landscape genetics approach. Both species are widespread throughout flood prone areas of arid and semi-arid Australia. Leaves were collected from 144 lignum plants across 10 sites and 84 river cooba plants across six sites, on the floodplain of the lower Lachlan Catchment, NSW. DNA was extracted and genotyped using DArTseq platforms. Genetic diversity and differentiation were compared with geographic distance and flooding frequency. It was found that genetic connectivity increased with increasing flooding frequency in lignum but not in river cooba. In lignum, sites that experience more frequent flooding had higher levels of genetic diversity and were more genetically homogenous. There was also an isolation by distance effect where increasing geographic distance correlated with increasing genetic differentiation in lignum, but not in river cooba. Waterbirds may play an important role in the dispersal of lignum, as water dispersal alone does not explain connectivity between patches. These data demonstrate how genetic patterns can highlight influential mechanisms over species distribution and persistence on floodplains.