Despite having many historically reported ethnomedicinal uses, Centaurium erythraea Rafn (Rafn and Buchs, 1800; common centaury) also produces cytotoxic secondary metabolites, and its presence should be carefully monitored. In this study, the complete chloroplast of Centaurium erythraea subsp. majus (Hoffmanns. & Link) M.Laínz (Laínz, 1971) isolate BPTPS121 is described, being the first available plastome belonging to the Centaurium genus. The chloroplast genome (GenBank accession number: ON641347) is 153,107 bp in length with 37.9% GC content, displaying a quadripartite structure that contains a pair of inverted repeat regions (25,166 bp each), separated by a large single-copy (84,388 bp) and small single-copy (18,387 bp) regions. A total of 129 genes were predicted, including 37 tRNA genes, eight rRNA genes, and 84 protein-coding genes. The phylogenetic analysis showed that isolate BPTPS121 is placed under the Gentianaceae family, belonging to the Gentianales order. The maximum-likelihood tree supports the already described lineage divergence in the Gentianaceae family, with C. erythraea subsp. majus belonging to the Chironieae tribe positioned below the Exaceae tribe and above the Potalieae and the entire Gentianeae tribes. This study will contribute to conservation, phylogenetic, and evolutionary studies, as well as DNA barcoding applications for food, feed, and supplements safety purposes.