The formation of skeletal structures composed of different calcium carbonate polymorphs (aragonite and calcite) appears to be regulated both biologically and environmentally. Among environmental factors influencing aragonite and calcite precipitation, changes in seawater conditions – primarily in the molar ratio of magnesium and calcium during so-called “Calcite” (mMg:mCa below 2) or “Aragonite” seas (mMg:mCa above 2) – have had profound impacts on the distribution and performance of marine calcifiers throughout the Earth’s history. Nonetheless, the fossil record shows that some species appear to have counteracted such changes and kept their skeleton polymorph unaltered. Here, the aragonitic octocoral Heliopora coerulea and the aragonitic scleractinian Montipora digitata were exposed to Calcite Sea-like mMg:mCa with various levels of changes in magnesium and calcium concentration, and both mineralogical (i.e., CaCO3 polymorph) and gene expression changes were monitored. Both species maintained aragonite deposition at lower mMg:mCa ratios, while concurrent calcite presence was only detected in M. digitata. Despite a strong variability between independent experimental replicates for both species, the expression for a set of putative calcification-related genes, including known components of scleractinian skeleton organic matrix, was found to consistently change at lower mMg:mCa. These results support previously proposed involvements of the skeleton organic matrix in counteracting decreases in seawater mMg:mCa. Although no consistent changes in expression for calcium and magnesium transporters was observed, down-regulation calcium channels in H. coerulea in one experimental replicate and at a mMg:mCa of 2.5 might indicate the possibility of active calcium uptake regulation by the corals under altered mMg:mCa open.