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Oberonia seidenfadenii is a rare and newly recorded plant species in Zhejiang province, China. In our present study, the complete chloroplast (cp) genome sequence of O. seidenfadenii was assembled by using high-throughput Illumina sequencing data. The plastome is 143,062 bp in size, which contains a typical quadripartite structure with a pair of inverted repeats (IR) regions (24,278 bp) separated by a small single-copy (SSC) region (10,224 bp) and a large single-copy (LSC) region (84,282 bp). The cp genome sequence contains 127 genes, including 74 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 7 pseudogenes. Phylogenetic analysis results indicated O. seidenfadenii is a sister of Oberonia japonica, with a support rate of 100%.