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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 0.636 with only the lowest value differing significantly from the others (Spop = 0.547). This indicated that there is a significant degree of variation within each population, and did not provide evidence for genetic 'bottle-neck' effects within the species. A pairwise distance measure calculated from the RAPD data was used as an input for principal coordinate (PCO) and AMOVA analyses. The first three principal coordinates of RAPD distances described 8.3, 5.9 and 5.4% of the total variance, respectively, and a degree of clustering of samples according to their geographical origin was detectable. AMOVA analysis indicated that although most of the variation (85.6%) was found within populations, a significant proportion (P < 0.002) was attributable to differences between populations. An UPGMA dendrogram constructed using phi ST values derived from AMOVA produced a pattern broadly similar to that produced by the PCO, highlighting differences between three main groups of populations within Chile: those from the northern Coastal Range, the southern Coastal Range and Central Depression, and the Andes. Populations from Argentina also emerged as significantly different from those in Chile. These results are interpreted in the context of the postglacial history of the species, and their implications for the development of conservation strategies for Fitzroya are discussed.