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Gillenia trifoliata (L.) Moench is an ornamental and medicinal species endemic to North America. In this study, a complete circular chloroplast genome of G. trifoliata was assembled and annotated. The chloroplast genome of G. trifoliata is 159,496 bp in size and consists of two IR (26,394 bp) regions separated by LSC (87,647 bp) and SSC (19,061 bp) regions. The GC content of the chloroplast genome is 36.5%. The chloroplast genome comprised of 112 different genes, including 78 protein-coding genes. The phylogenetic analysis revealed that G. trifoliata lies within subfamily Amygdaloideae and forms the progenitor lineage of the pome-bearing Maleae.