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Styrax japonicus is a shrub with high economic values. Here, complete chloroplast (cp) genomes were reported using high-throughput Illumina sequencing. The size of the S. japonicus chloroplast genome is 157,940 bp long, with an average AT content of 63.05%, containing a pair of inverted repeats of 24,047 bp, separated by a large single copy and a small single copy region of 87,562 bp and 22,284 bp, respectively. It contains 125 genes, including79 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. A maximum-likelihood phylogenetic tree supported the fact that the chloroplast genome of S. japonicus is closely related to that of Symplocos paniculate.