Eucalyptus marginata faces many threats across its native range in southwestern Australia, including potential impacts from climate change. Ongoing reforestation efforts provide an opportunity to establish resilient forests by selecting seeds that are adapted to predicted future climates, as well as current conditions. We use genotyping-by-sequencing (GBS) methods to genotype hundreds of trees from transects across a rainfall gradient. Models of isolation by distance and isolation by environment provide valuable information on the processes that drive patterns of genomic variation across the landscape, with important implications for seed sourcing. Weak isolation by distance indicates that provenancing does not have to be strictly local. Environmental association suggests that assisted migration of seeds over longer distances might be necessary given future climate change scenarios.