The impact of past anthropogenic disturbance on the amount and distribution of genetic diversity is a key factor in determining the resilience of tree species to environmental change. This is particularly the case for narrowly distributed species where disturbance has impacted most of the species’ range. Here we examine the legacy of post-colonial logging and fire on patterns of genetic diversity in the Tasmanian palaeoendemic conifer Lagarostrobos franklinii (Podocarpaceae), a fire sensitive and slow growing rainforest tree valued for its durable timber. Thirty-three populations (12 of which represent primary stands) from across the species range were genotyped using eight nuclear SSRs (871 samples) and MIG-seq-based single nucleotide polymorphisms (254 samples). Genetic differentiation was relatively high for conifers (Fst of 0.113 and 0.143 for nuclear SSR and MIG-seq, respectively) with cryptic divergence between populations geographically close but in differing river catchments likely reflecting postglacial dispersal from distinct Last Glacial refugia and low levels of gene flow. Population level genetic diversity was greatest in the core of the range with no significant correlation with the history of post colonial human disturbance (i.e. primary vs. non primary stands) and, unexpectedly, given the greater impact of logging at lower elevations, a significant decline in allelic richness with elevation. Overall, this study shows that L. franklinii has been resilient to past timber exploitation and uncovers previously undetected genetic patterns. This shows that genetic tools can be invaluable in characterising species specific impacts of disturbance and in helping guide the ongoing conservation of important species.