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Lemmaphyllum intermedium is a valuable medicinal fern in China. We have determined its complete chloroplast genome using Illumina paired-end sequencing. The genome is 157,795 bp in length with 132 genes, including 88 protein-coding genes, eight ribosomal RNA genes, 35 tRNA genes, and one pseudogene. It has a quadripartite structure consisting of a small single-copy (SSC) of 21,764 bp, a large single-copy (LSC) of 81,189 bp, and two inverted repeats (IRs) of 27,421 bp each. A maximum-likelihood phylogenetic tree reconstructed by using complete chloroplast genome sequences reveals that L. intermedium is closely related to Lemmaphyllum carnosum var. microphyllum with strong support.