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Waldheimia glabra (Decne.) Rgl. 1879 (family Asteraceae) is a perennial herb with high economic and medicinal values. In this study, we sequenced the complete chloroplast (cp) genome of W. glabra by high-throughput Illumina sequencing. The size of the W. glabra cp genome is 151,499 bp, with overall GC content of 37.3%. It contains a large single copy and a small single copy region of 83,078 bp and 18,457 bp, respectively, separated by a pair of inverted repeats regions of 24,982 bp. We also discovered 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes in the genome. The maximum-likelihood phylogenetic tree demonstrated that W. glabra is closely related to Leucanthemella linearis.