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Dolomite is abundant in geological settings, but rarely forms under laboratory conditions at room temperature, not even in highly supersaturated solutions. The solution to the issue of how dolomite forms at low temperatures depends on observations of natural samples. Here, the Pleistocene dolostones from the Mischief Atoll in the South China Sea were investigated to demonstrate the process by which dolomite replaces calcite at low temperatures. The dolostones in the Mischief Atoll are composed of dolomite matrix, dolomite cement, pore-lining dolomite, and pore-lining calcite. The focus of this paper is to examine the crystal-scale process by which pore-lining dolomite replaces pore-lining calcite. Transmission electron microscope analyses of the replacive dolomite show the inheritance of crystal shape and lattice orientation from the primary calcite, a sharp and coherent interface with the primary phase, abundant nanopores at the replacement front, and residual calcite in the dolomite. These observations collectively support a coupled dissolution-reprecipitation mechanism operating at the replacement front. In the replacive dolomite, nanopores are absent in the part far from the replacement front. This part of the replacive dolomite is characterized by a morphologically modulated or tweed structure. A modulation process involving nanopore infilling and morphological adjustment has occurred at the replacement front. Through continuous dissolution, precipitation, and modulation, the replacement front between dolomite and calcite progresses into the calcite crystal until it is completely replaced by dolomite. This study elucidates the process by which dolomite replaces calcite in natural settings and provides a realistic basis for experimental and modeling studies of dolomite growth.