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Bolbitis multipinna is an endemic fern found in Yunnan, China. In the case of the chloroplast genome, Illumina Hiseq X-Ten was used, and it revealed a conserved quadripartite structure of 152,437 bp, including a large single-copy (LSC) region of 82,618 bp, a small single-copy (SSC) region of 21,403 bp, and a pair of inverted repeat regions of 24,208 bp (IRa and IRb). The chloroplast genome of B. multipinna contains 132 genes, including 89 protein-coding genes, 35 tRNA genes, and eight rRNA genes. By using the maximum-likelihood method and the Bayesian analysis on the chloroplast genomes of 15 species ferns, the phylogenetic analysis revealed that B. multipinna is closely related to B. heteroclita.