Hydroxyapatite (HAp) is a bio-ceramic material in the family of calcium phosphate. Due to its biocompatibility nature, it is used widely for bone regeneration, orthopedic implants, development of dental materials, and also used in environmental applications. HAp can be prepared using both chemical precursors and natural sources. Chemical precursors of calcium and phosphate are commonly used in synthesis of HAp via various methods such as wet, dry, hydrothermal and precipitation, emulsion, freeze-drying, and electrochemical deposition, among others. However, it affects human cells slightly when using the chemical precursor-mediated synthesis of HAp. Therefore, many researchers have been focusing on natural source materials or biological synthesis methods rather than the chemical methods. So, it is necessary to synthesize toxic free materials from natural bio-waste materials that have been converted into valuable bio-compounds. Natural derived HAp has been applicable for various biomedical applications due to its excellent biocompatibility, bio-degradability and bioactivity nature. This review discusses the recent development of derived HAp from various natural sources, including marine, mammalian and shell sources, for biomedical applications particularly in bone tissue engineering.