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Fitzroya cupressoides (alerce, Cupressaceae) is a large and exceptionally long‐lived conifer, endemic to a restricted area of southern Chile and neighbouring areas of Argentina. As a result of its high economic value, the species has been severely exploited for timber, and remnant populations are fragmented and often highly disturbed. The species is thought to have undergone a major range contraction during the last glaciation. In order to assess the extent of genetic variation using DNA markers within and between populations of this species, samples were obtained from throughout the natural range and analysed for random amplified polymorphic DNA (RAPD) variation. Eight 10‐mer and three 15‐mer primers were used to produce a total of 54 polymorphic bands. Shannon's diversity estimates were calculated to provide an estimate of the degree of variation within each population. Values varied from 0.343 to …