Carbonated apatite, the basic mineral component in human hard tissues and an important bioceramic material, has been extensively studied. However, its atomic arrangements in apatite crystal structure and its experimental characterization are still not lack of debating. We analyzed infrared (IR) vibrational spectroscopy for carbonated apatite determinations, by comparatively studying the IR spectra of hydroxyapatite and of surface carbonate absorption, biological apatites (human enamel, human cortical bone, and two animal bones) and carbonated apatite. The carbonated apatite samples were sythesized by various methods, including precipitation method, hydrothermal reaction and solid-gas reaction at high temperature. The comparative study indicates that the bands at ~880 cm-1, ~1413 cm-1, and ~1450 cm-1 should not be used to identify carbonated apatite since they may result from carbonate absorption on surfaces of apatite crystals or separated carbonate phase present with apatite crystals. The IR characteristic bands of carbonate substitution in apatites should be: ν3 at ~1465 cm-1 for type-B (CO3 substituting for PO4) and ν3 band at ~1546 cm-1 for type A (CO3 substituting for OH). These signature IR bands are further confirmed by the ab initio simulations.