Nothofagus moorei is a long-lived, Gondwana relict cool temperate rainforest tree. Nothofagus-dominated rainforests were widespread across much of eastern Australia during the mid-Tertiary but today, N. moorei occurs only as a series of disjunct, isolated populations in south-east Queensland and northern New South Wales. Clonal regeneration via coppicing is reported to be a common feature of most N. moorei populations, while successful sexual regeneration is believed to be rare, occurring largely only in niches with high light levels and limited competition. While clonal propagation enables population persistence and individual longevity, it cannot generate novel genotypes. Isolated populations, potentially high levels of clonality, low-potential for successful sexual regeneration, long-lived individuals and predicted global warming effects make N. moorei vulnerable to local, if not total, population extinction. The current study aimed to assess the relative conservation status of extant N. moorei populations in order to develop appropriate conservation management strategies for long-term population persistence. Levels of genetic diversity and population structure were examined across the remaining natural distribution of N. moorei using nuclear amplified fragment length polymorphism (AFLP), microsatellite and chloroplast DNA markers. In total 607 individuals were sampled from 20 populations and 5 geographical regions: Lamington/Border Ranges, Ballow, Dorrigo/New England, Werrikimbe and Barrington. Genetic results were then analysed to assess conservation status of each population and geographical region. Microsatellite and AFLP data identified comparatively high levels of genetic diversity in all remnant populations sampled. The prevalence of coppicing in the northern Lamington/Border Ranges populations appears to have had little impact on relative levels of genetic diversity, heterozygosity or population structure. Population differentiation was limited, with the majority of genetic variation retained within populations, no regional structuring and high levels of admixture. Analysis of cpDNA variation showed that the three Dorrigo/New England populations were divergent from all other populations, suggesting an ancient divergence in N. moorei prior to Pleistocene glaciations. While levels of genetic diversity were essentially the same across all populations, Bayesian analysis of genetic structure did identify four populations with differing gene pool proportions which would be important to include in conservation efforts in addition to individuals from other populations. Similarly, individuals from four significantly differentiated groups identified using traditional F-statistics suggests individuals from each of these four groups should be included in future conservation plans. In order to maintain ancient chloroplast lineages, populations from the Dorrigo/New England region should also be assigned special conservation value. Populations of N. moorei appear to have retained significant levels of genetic diversity and show little population divergence in spite of marked reductions in the natural distribution since the Early Miocene. Sampling of these ancient trees however, suggests current levels of diversity in N. moorei actually reflect past diversity and differentiation, and that there have been insufficient generations since the historical contraction in distribution for genetic diversity to be adversely affected and regional differentiation to evolve. Long-term persistence of N. moorei is still threatened by future accelerated climate change and the limited preferred habitat that remains where N. moorei can expand its range. While the ability to regenerate clonally may enable long-term persistence of N. moorei, populations are still likely to continue to decline as climatic conditions will increasingly favour sub-tropical and warm temperate species across much of N. moorei's northern distribution. Southern populations of N. moorei, in contrast, could expand their ranges into eucalypt woodlands as predicted climate becomes warmer and wetter. However, this will ultimately be determined by the frequency of fires, with increased fire frequencies favouring the expansion of eucalypts and contraction and possible local population extinction of N. moorei dominated cool temperate rainforests.