Shorea javanica is an economically important dammar-producing tree, endemic to tropical lowland forest in Sumatra and Java, Indonesia. Total population size, however, is very limited and endangered. We sequenced three non-coding regions of chloroplast DNA and three nuclear genes, and genotyped seven microsatellite loci in six populations representing the current species distribution. There was no variation in the chloroplast DNA regions, except for one unique indel polymorphism. Mean silent site nucleotide diversity across three nuclear regions was 0.0011, which is much smaller than those of common dipterocarp species. Expected mean population heterozygosity in the microsatellite loci was 0.423, and the total heterozygosity was 0.477. These results show genetic variation in S. javanica is extremely low at both population and species levels. Genetic differentiation among populations was moderate (FST = 0.064 for nuclear genes and FST {ENA} = 0.076 for microsatellite loci), but this result is essentially caused by one isolated population in Oku. We suggest that conservation efforts should focus on promoting connectivity and augmenting population size across the species range. Ex-situ conservation should also be considered to provide insurance against catastrophic events and to facilitate for reintroduction.   Key words: Shorea javanica, repong dammar, chloroplast DNA, nuclear genes, microsatellite markers.

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