Aleurites moluccana is an evergreen broad-leaved tree of the genus Aleurites in the family Euphorbiaceae, with energy, medicinal and ornamental values. To fill the gap in study of the chloroplast genome of A. moluccana, we assembled and annotated the chloroplast genome of A. moluccana by next-generation high-throughput whole genome sequencing, and performed genomic characterization and phylogenetic analysis. The results showed that the chloroplast genome of A. moluccana exhibited typical quadripartite and circular structures with a total length of 163 298 bp, the length of LSC, SSC, and IR was 91 301, 18 501, and 26 748 bp, respectively. It contains 131 genes, including 8 rRNA genes, 37 tRNA genes and 86 protein coding genes. A total of 145 SSR loci were found, with mononucleotide, dinucleotide, trinucleotide and tetranucleotide repeat units, and the numbers detected were 80, 53, 10, and 2, respectively. The results of collinearity analysis showed that the chloroplast genome of A. moluccana has the phenomenon of gene inversion and rearrangement. Phylogenetic trees were constructed using the maximum likelihood and Bayesian methods. It was found that A. moluccana was closely related to Vernicia fordii and Deutzianthus tonkinensis, and formed a sister group. The results of the dating analysis using fossil time showed that the differentiation time of the Aleurites, Vernicia and Deutzianthus was 25.94 Ma (95% HPD: 24.71-63.32 Ma). This study enriched the genomic information of A. moluccana and provided basic genetic data for the development and utilization of A. moluccana germplasm resources, as well as a reference for species identification and phylogenetic study of the Aleurites.