Apatite is the most abundant phosphate mineral on Earth and forms the foundation of the global phosphorus cycle. Interest in apatite crosses many disciplines, including geology, agriculture, material science, dentistry, and medicine, and the phase is also used extensively in many manufacturing processes. Apatite is the main source of phosphate for fertilizer, and adequate sources of apatite are essential for production of fertilizers that are necessary for feeding the world’s population. Despite the importance of the phase, the atomic arrangement of apatite is not well understood. The natural apatite anion solid solution among F, OH, and Cl (fluorapatite, hydroxylapatite, and chlorapatite, respectively) is one of those rare solid solutions wherein the atomic arrangements of the binary and ternary solid solutions are not predictable from the atomic arrangements of the endmembers of the ternary system; the steric interactions in the (F, OH, Cl) apatite anion column are complex as the three anions mix. Although the first detailed account of the atomic arrangement of binary apatites along the F-Cl join was recently reported using painstakingly synthesized samples, natural Cl-rich fluorapatite, although long-sought, had not been identified; an Earth environment that has high fugacity of F and Cl, but is devoid of OH, is rare. Here we report the atomic arrangement of a natural Cl-rich fluorapatite from the Three Peaks area of Utah (USA) that is essentially devoid of OH. The structure (R1 = 0.0145) of the P63/m apatite is similar to that obtained from synthetic samples, and demonstrates that solid solution along the F–Cl join in natural apatites is achieved by creation of a second F site (Fb) in the Cl-rich fluorapatite [0, 0, z] anion column, an off-mirror site at z = 0.178, coupled with the presence of a site for Cl (Clb), that differs from the Cl site in endmember chlorapatite. The combination of a Cl site that relaxes toward its associated mirror plane and a neighboring F site that relaxes away from its associated mirror plane allows sufficient separation of F and Cl in the anion column for the two anions to coexist. The structure described herein is the first reported structure of a natural Cl-rich fluorapatite.