Transmission electron microscopy (TEM) and molecular simulation studies of traces of chemical elements such as Mg, Si, and OH in the hydroxylapatite (CaHAP) crystal structure obtained from the sand dollar were carried out. Two different types of CaHAP crystal morphologies in the samples synthesized by the hydrothermal method used were observed. Reflections with regular intensity in the experimental electron diffraction patterns obtained from these morphologies were observed. However, when these results were compared with a simulated electron diffraction pattern (which was obtained using the crystalline structure proposed for the hydroxylapatite) some forbidden reflections in the experimental pattern were observed. Then, in order to reproduce the experimental patterns Si and Mg atoms in the crystalline lattice were introduced. These elements in the elemental chemical analysis carried out by X-ray energy dispersive spectroscopy (EDS) in the typical CaHAP morphologies were detected. The positions of these atoms in the asymmetric unit were obtained using molecular simulation and during the relaxation process, the structure did not show changes in the lattice parameters. Subsequently, the crystalline structure was reproduced and matched the electron diffraction patterns simulated resulting in the experimental electron diffraction pattern. Experimental and simulated X-ray diffraction spectra were also matched.