AbstractLithocarpus konishii, a rare species endemic to islands in South China, was evaluated as a vulnerable species (VU) by the ‘China Species Red List.’ Here, we first presented the complete chloroplast genome sequence ofL. konishii.The chloroplast genome was 161,059 bp in length with 36.76% GC content, containing a small single-copy region (SSC, 18,967 bp), a large single-copy region (LSC, 90,250 bp), and a pair of inverted repeats (IRs, 25,921 bp each). A total of 139 genes were predicted, including 87 protein-coding genes (CDS), 8 rRNAs, and 44 tRNAs. Based on the concatenated shared unique CDS sequence dataset, maximum-likelihood and Bayesian inference methods were used to build the phylogenetic trees of 18 species from the Fagaceae family. Results indicated thatL. konishiiis closely related toL. longnuxandL. pachyphyllusvar.fruticosus, and forms a monophyly of the subfamily Castaneoideae withCastanopsisandCastanea. This study provides a theoretical basis for the conservation genomics of this endangered plant.