Rainforests in Australia and around the world have been extensively cleared and degraded. It is essential to recognize the changes in population diversity and dynamics that follow habitat fragmentation if better conservation and management strategies are to be developed. This study is an investigation of the medium term (over 100 years) effects of rainforest fragmentation on a long-lived, early successional tree species within a habitat matrix that includes various types of fragmented and undisturbed sites. Five microsatellite loci were used to assess the level and distribution of genetic variation across the southern range of Elaeocarpus grandis (Elaeocarpaceae). In all, 21 sites were sampled to provide a direct comparison between fragmented and undisturbed populations. Overall levels of diversity (A=3.4, He=0.568, f=0.094) were higher than those of closely related endemic species, but lower than those recorded across other rainforest trees. No significant genetic structure was detected across this species, suggesting the existence of efficient dispersal and colonization mechanisms responsible for the maintenance of gene flow. Rainforest fragments, and in particular those within the extensively cleared Big Scrub, show a trend for increased inbreeding levels caused by a loss of heterozygosity within juvenile cohorts. However, the overall rate of genetic decline within fragmented rainforests appears to be more subtle in E. grandis than across other species. A combination of ecological attributes and evolutionary history is likely to have contributed to this outcome and need to be considered in future rainforest restoration projects.