Under microwave irradiation, carbonated hydroxyapatite (CHAp) was prepared by a unique method using goniopora as calcium precursor and di-basic calcium phosphate (CaHPO4) as phosphate precursor. The final products were characterized by X-ray powder diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, and thermogravimetric (TG) analysis. The XRD pattern confirms the formation of hydroxyapatite (HAp) without detecting any extraneous phases. The FT-IR spectrum of HAp shows trace element of carbonate ions indicating carbonate substitution into the apatite phase. The goniopora was found to decompose all the organic debris and carbonate phases at 900°C. The prepared CHAp shows no significant weight loss up to 1000°C indicating its thermal stability. In-vitro solubility test show increase in the CHAp solubility than pure HAp. These findings imply the feasibility of CHAp formation using goniopora under microwave irradiation. The prepared CHAp can be used as a potential bone substitute since it resembles biological apatite in view of physico-chemical properties.