1. In much of the world, fauna has been adversely affected by human actions, including conversion of forests to farmland, logging and regulation of river flows. Landscape genetics data can provide information about dispersal and gene flow across the landscape, identifying barriers and facilitators of gene flow. Landscapes of central Victoria, Australia, have been altered extensively in the last 160 years. Much vegetation has been cleared or degraded, and only forest patches of mainly re-growth remain, yet some forest-dependent species like the yellow-footed antechinus Antechinus flavipes persist. The antechinus has good dispersal capabilities and is the only native, small, carnivorous mammal on most floodplains. We use antechinus as a model to understand species persistence in fragmented landscapes. 2. We analysed variation at 11 microsatellite loci and the control region of mitochondrial DNA to infer past and contemporary gene flow among A. flavipes populations. To explore genetic connectivity, we used least-cost path methods, which assign different ‘friction’ costs to vegetation, cleared land, roads and rivers. 3. Populations from 11 forests formed six distinct genetic groups, and with few exceptions, animals from nearby forests clustered together despite the intervening Murray River or farmland with only narrow vegetation corridors between them. 4. Genetic connectivity was aided by corridors of vegetation and inhibited by cleared land. 5. Synthesis and applications. Our approach, capitalizing on inferences on both historic and contemporary gene flow, provides management agencies with key information on metapopulation dynamics in landscapes. Rather than merely maintaining existing vegetation upon which this (and many other) species depend, the genetic information also informs where future plantings should be prioritized to facilitate demographic and genetic exchange among sub-populations of species. Moreover, the decline in condition (‘health’) of riparian trees in this region must be reversed by provision of flooding flows; otherwise, metapopulation dynamics will become even more disarticulated than at present.