Limestone is an important commodity in Philippines. Limestone has numerous uses that range from agricultural applications to building materials to medicines. Many limestone products require rock with specific physical and chemical characteristics. Most limestone is biochemical in origin meaning the calcium carbonate in the stone originated from shelled oceanic creatures. In this paper, we reported the natural sources of limestone, geological formation of limestone and the oyster shell waste in Cebu, Bantayan, Philippines were reported. Due to the mining or quarrying in Cebu, Bantayan, in a limestone area poses the threat of groundwater pollution (since limestone is a porous geologic formation with a high transmissivity). The other environmental issue is oyster shell waste. The oyster shell waste is the major source of limestone. We developed and applied appropriate technologies for the extraction of limestone from oyster shell waste and utilizes as high value added material.