A porous hydroxyapatite has been prepared using natural coral which resembles human cancellous bone in microstructure. To obtain a biomaterial having a good biocompatibility, substitution of silicon into the hydroxyapatite framework has been attempted. Si substituted hydroxyapatite has been prepared by hydrothermal treatment and solvothermal treatment of the natural coral repeatedly. Si concentration and phase of the Si substituted hydroxyapatite derived from coral have been characterized using a XRD, ICP, and EDS etc. EDS investigation confirmed the presence of silicon in the framework of hydroxyapatite structure.