All known populations of the nationally critical tree daisy, Olearia gardneri, were studied using AFLP markers. With fewer than 160 individual plants, Olearia gardneri is the third-rarest tree in New Zealand and a good model with which to study evolutionary process in fragmented endangered plants. Genetic variation was at similar levels to other long-lived tree species in New Zealand and also as in other studies to date had poor correspondence between genetic and geographic distance. Genetic factors such as inbreeding depression and the loss of genetic diversity might lower fitness and have substantial consequences for evolution and survival of rare threatened plants. Due to the decline of this species in recent times it is imperative that conservation measures are undertaken, including revegetation. Despite considerable emphasis on ''eco-sourcing'' in plant recovery programmes there is strong evidence that this may not be the best strategy for O. gardneri due to breeding system and population size considerations.