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Background  The need to incorporate genetic data into conservation management decisions is increasingly recognised. However, many published studies represent a ‘gold standard’ of sampling, techniques, and analyses. Such rigour is often not possible with limited funding and resourcing available for developing plans for the increasing number of threatened species requiring conservation management. Two endemic palm species of the Itremo Massif in central Madagascar,  Dypsis ambositrae  and  D. decipiens , are known to be threatened with extinction and conservation management for these species is a priority for the newly created protected area in the region.    Methods  The genetic diversity of these two species was studied using the relatively low-cost and rapid AFLP technique. DNA fragments generated using three primer combinations were analysed for 20 and 50 individuals of the two species, respectively, from across their ranges.    Results  Genetic diversity was relatively low for both species. The two sites where the highly restricted  D. ambositrae  grows were found to be genetically distinct (although overall heterozygosity was low). Despite having a much wider distribution and relatively large population,  D. decipiens  did not show clear geographical nor genetic groupings and had similarly low genetic heterozygosity to  D. ambositrae .    Discussion and Recommendations  With so few individuals remaining in the wild and two genetically distinct subpopulations, it is recommended that both sites of  D. ambositrae  are conserved and that seed are collected from both for  ex situ  conservation and potential future reintroduction. It may be less important to focus resources on conserving or collecting  ex situ  material from all sites where  D. decipiens  is found, as the genetic diversity represented by each subpopulation is limited and increasing sampling may not protect significantly higher levels of genetic diversity. This study provides data that inform and support conservation decisions taken for both species within this region, and in the management of the newly designated Itremo Massif Protected Area, which covers most of the sites where these two species remain in the wild.

Population genetics data help to guide the conservation of palm species with small population sizes and fragmented habitats in Madagascar