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Aquilaria crassna Pierre ex Lecomte is a principal agarwood tree resource. It has been listed as a critically endangered species. The complete chloroplast genome of A. crassna was assembled based on next-generation sequencing. The plastome was a quadripartite circular shape with 174,830 bp in length, including a large single-copy (LSC) region of 87,450 bp and small single-copy (SSC) region of 3346 bp, separated by two inverted repeat (IR) regions of 42,017 bp each. The chloroplast genome contained 125 genes, including 79 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the whole genome was 36.7%. The phylogenetic tree showed that three species of Aquilaria formed one monophyletic clade with 100% bootstrap value.