This review summarizes recent work on isolating and preparing bioapatites from various natural sources. First, the physicochemical properties of bioapatites are described and discussed. Then, a general summary of natural (animals and vegetals) sources for bioapatite production from various environments (terrestrial and water) is made. Special attention is paid to describing individual methods for acquiring bioapatite from biogenic sources, e.g., direct isolation of bioapatite, or indirect biomimetic synthesis, with the aid of naturally derived biomolecules or biomembranes. The results of a comprehensive physicochemical characterization and a biological evaluation (in vitro and in vivo) for bioapatites and their applications in clinical practice are presented. Finally, future perspectives are summarized and discussed.