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DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers <i>matK</i>, <i>rbcL</i>, and <i>trnL-F</i>, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene <i>matK</i> was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of <i>Anthoshorea</i>, <i>Hopea</i>, <i>Richetia</i>, <i>Parashorea</i>, and <i>Anisoptera</i>, nonetheless these markers were inefficient to resolve the relationships within the <i>Rubroshorea</i> group. The maximum likelihood and Bayesian inference phylogenies identified <i>Shorea</i> as a paraphyletic genus, <i>Anthoshorea</i> appeared as sister to <i>Hopea</i>, and <i>Richetia</i> was sister to <i>Parashorea</i>. A better discriminatory power among dipterocarp species provided by <i>matK</i> and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.