The threatened Chilean conifer Podocarpus salignus D. Don is currently the focus of ex situ conservation eorts being undertaken by the Conifer Conservation Programme of the Royal Botanic Garden Edinburgh. To assess variation within in and ex situ populations of the species, leaf material collected from four wild populations was analysed by random amplified polymorphic DNA (RAPD). Amova of RAPD profiles indicated that 93% of the variation occurred within, rather than between, populations. Intraspecific genetic diversity, estimated using percentage polymorphic loci, Shannon's diversity index, and Nei's gene diversity, was relatively high (47%, 0.692 and 0.314, respectively). To assess genetic diversity in ex situ populations within the UK, RAPD analysis of parents and progeny at two Cornish arboreta was undertaken. The results provided evidence of novel hybridization with suspected paternal trees (P. hallii Kirk and P. totara G. Benn. ex D. Don) endemic to New Zealand. RAPD was found to be an effective tool for assessing the genetic structure of P. salignus, for providing a guide to future germplasm-sampling strategies, and for hybrid identification. Implications for genetic conservation of the species and the role of ex situ approaches are discussed.