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Goodyera schlechtendaliana is a common orchid species in East Asia. A distinctive population of G. schlechtendaliana with the lateral appendages of the column in their flowers was found in southwestern Korea. In this study, we presented complete chloroplast genome of this morphotype as a part of systematic study of the Goodyera. The chloroplast genome is 153,882 bp in length and contains 134 genes (83 CDSs, 8 rRNAs, and 39 tRNAs). Phylogenetic analysis showed that the morphotype of G. schlechtendaliana with column appendages is sister to a normal form of G. schlechtendaliana with long branch, supporting that this distinctive morphotype has a potential to be a new species.