We propose a microscopic model of the dominant carbonate for phosphate substitution in fluor- apatite. A well-crystallized sedimentary fluorapatite sample containing ~2.3 ± 0.8 wt% of carbonate was investigated using Fourier transform infrared spectroscopy (FTIR) and ¹³C and ¹⁹F magic angle spinning nuclear magnetic resonance (MAS NMR). About 75% of the carbonate groups replace the phosphate group ("B-site"), whereas a lesser contribution from carbonate groups located in the structural channels ("A-site") is observed. Beside the dominant ¹⁹F NMR signal of channel ions at ~ -102 ppm, an additional signal corresponding to ~8% of fluoride ions is observed at -88 ppm. ¹⁹F double quantum-single quantum (DQ-SQ) MAS NMR and ¹³C{¹⁹F} frequency-selective Rotational Echo DOuble Resonance (REDOR) experiments prove that this additional signal corresponds to iso- lated fluoride ions in the apatite structure, located in close proximity of substituted carbonate groups. Density functional theory (DFT) calculations allow us to propose a composite carbonate-fluoride tetrahedron defect model accounting for these experimental observations. The planar carbonate ion lies in the sloping face of the tetrahedron opposite a fluoride ion occupying the remaining vertex, together replacing the tetrahedral phosphate ion. This "francolite-type" defect leads to a diagnostic narrow IR absorption band at 864 cmĐ¹ that could be used as a guide to, e.g., detect the incipient transformation of fossil bone and teeth samples.