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Histiopteris incisa is a core member to address the issue of relationship between Histiopteris and Pteris. Its complete chloroplast genome was generated by de novo assembly using Illumina sequencing. The complete chloroplast genome is a quadripartite structure of 16,0567 bp in length, with two inverted repeat regions (IRs) of 27,119 bp each, a large single-copy (LSC) region of 84,897 bp and a small single-copy (SSC) region of 21,432 bp. A total of 132 genes were predicted, involving in 88 protein-coding genes, eight rRNA genes, 35 tRNA genes, and one pseudogene. ML phylogenetic analysis showed that H. incisa was closely related to Pteridium aquilinum subsp. aquilinum.