The uptakes of calcium (Ca), strontium (Sr), and barium (Ba) by two cyanobacterial strains, Cyanothece sp. PCC7425 and Gloeomargarita lithophora, both forming intracellular carbonates, were investigated in laboratory cultures. In the culture medium BG-11 amended with 250 μM Ca and 50 or 250 μM Sr and Ba, G. lithophora accumulated first Ba, then Sr, and finally Ca. Sr and Ba were completely accumulated by G. lithophora cells at rates between 0.02 and 0.10 fmol h-1 cell-1 and down to extracellular concentrations below the detection limits of inductively coupled plasma atomic emission spectroscopy. Accumulation of Sr and Ba did not affect the growth rate of the strain. This sequential accumulation occurred mostly intracellularly within polyphosphate and carbonate granules and resulted in the formation of core-shell structures in carbonates. In contrast, Cyanothece sp. PCC7425 showed neither a preferential accumulation of heavier alkaline earth metals nor core-shell structures in the carbonates. This indicated that fractionation between alkaline earth metals was not inherent to intracellularly calcifying cyanobacteria but was likely a genetically based trait of G. lithophora. Overall, the capability of G. lithophora to sequester preferentially Sr and Ba at high rates may be of considerable interest for designing new remediation strategies and better understanding the geochemical cycles of these elements.