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Castanea seguinii is an endemic chestnut species in China, which is widely distributed over central and southeastern China. The chloroplast genome sequences were finally resolved by high-throughput sequencing platform Illumina Hiseq X Ten. Totally the genome is 160,419 bp in size, AT rich (63.3%), comprising a couple of 25,694 bp long inverted repeat regions, separated by a 90,055 bp large and 18,976 bp small single copy regions. 79 protein-coding genes, four ribosomal RNA genes and 30 transfer RNA genes were identified and annotated. The results of the molecular phylogenetic analysis exhibited that C. seguinii showed the closest relationship with C. mollissima, with high bootstrap support.