In this study, hydroxyapatite (HAp) was extracted from freshwater fish scales and saltwater fish scales using thermal decomposition method at various temperatures. The percentages of HAp in each species of raw fish scales were analysed using thermogravimetry analysis (TGA) whereas Fourier transform infrared (FTIR) was used to confirm the present of HA. The crystallinity of the HAp was studied using x-ray diffractometer (XRD). TGA and FTIR are found to be useful techniques to predict the composition of the HAp present in the fish scales. The results show that the composition of HAp in the fish scales was not significantly dependent on the species of the fish. The percentage of HAp in the fish scales ranged from 40 to 45 wt. The heating temperature had an effect on the crystallinity and colour of the HAp produced. Results from FTIR and XRD confirmed that the HAp extracted from fish scales was similar to the HAp standard. However, the natural HAp produced from saltwater fish scales was more crystalline than that produced from freshwater fish scales. The HAp produced from this study is relatively cheap and more importantly they are HALAL for four billion Muslims population around the world. © (2012) Trans Tech Publications, Switzerland.