Conservation management often uses information on genetic population structure to assess the importance of local provenancing for ecological restoration and reintroduction programs. For species that do not exhibit complete reproductive isolation, the estimation of population genetic parameters may be influenced by the extent of admixture. Therefore, to avoid perverse outcomes for conservation, genetically-informed management strategies must determine whether hybridisation between species is relevant, and the extent to which observed population genetic patterns are shaped by inter-specific versus intra-specific gene flow. We used genotyping-by-sequencing to identify over 2400 informative single-nucleotide polymorphisms across 18 populations of Eucalyptus regnans F. Muell., a foundation tree species of montane forests in south-eastern Australia. We used this data to determine the extent of hybridisation with another species, Eucalyptus obliqua L’Hér., and investigate how admixture influences genetic diversity parameters, by estimating metrics of genetic diversity and examining population genetic structure in datasets with and without admixed individuals. We found hybrid individuals at all sites, and two highly introgressed populations. Hybrid individuals were not distributed evenly across environmental gradients, with logistic regression identifying hybrids as being associated with temperature. Removal of hybrids resulted in increases in genetic differentiation (FST), expected heterozygosity, observed heterozygosity and the inbreeding coefficient, and different patterns of isolation-by-distance. After removal of hybrids and introgressed populations, mountain ash showed very little population genetic structure, with a small effect of isolation-by-distance, and very low global FST (0.03). Our study shows that, in plants, decisions around provenancing of individuals for restoration depend on knowledge of whether hybridisation is influencing population genetic structure. For species in which most genetic variation is held within populations, there may be little benefit in planning conservation strategies around environmental adaptation of seed sources. The possibility for adaptive introgression may also be relevant when species regularly hybridise.