The crystal structure of carbonate containing apatite from albid tissue of Late Devon conodonts of Polygnathus species (Ozarkodinida order) has been refined by single crystal X-ray diffraction with the application of electronprobe X-ray microanalysis and Raman spectroscopy data. This apatite–organic composite yields a diffraction pattern characteristic of a single crystal. The atomic structure of biological apatite is close to that of stoichiometric apatite(CaF). The content of carbonate ions replacing [PO4]3– anions is very low (~1 wt %). Channels of the structure contain not only fluorine but also OH ions (in a ratio of 3 : 1); the latter are partially replaced with water molecules. The main cationic substitutions occur in the Ca2 position. The specific features of the diffraction pattern of albid tissue indicate that the apatite–organic composite under study is a nanostructured material (a biological mesocrystal).