Understanding whether populations can adapt in situ or whether interventions are required is of key importance for biodiversity management under climate change. Landscape genomics is becoming an increasingly important and powerful tool for rapid assessments of climate adaptation, especially in long-lived species such as trees. We investigated climate adaptation in Eucalyptus microcarpa using the DArTseq genomic approach. A combination of FST outlier and environmental association analyses were performed using > 4,200 genome-wide single nucleotide polymorphisms (SNPs) from 26 populations spanning climate gradients in south-eastern Australia. Eighty-one SNPs were identified as putatively adaptive, based on significance in FST outlier tests and significant associations with one or more climate variables related to temperature (70 / 81), aridity (37 / 81) or precipitation (35 / 81). Adaptive SNPs were located on all 11 chromosomes, with no particular region associated with individual climate variables. Climate adaptation appeared to be characterized by subtle shifts in allele frequencies, with no consistent fixed differences identified. Based on these associations, we predict adaptation under projected changes in climate will include a suite of shifts in allele frequencies. Whether this can occur sufficiently rapidly through natural selection within populations, or would benefit from assisted gene migration, requires further evaluation. In some populations, the absence, or predicted increases to near fixation of particular adaptive alleles hint at potential limits to adaptive capacity. Together, these results reinforce the importance of standing genetic variation at the geographical level for maintaining species’ evolutionary potential.