We analyzed shell cuts of five individuals of the Antarctic bivalve Laternula elliptica from three locations along the Antarctic Peninsula by means of Confocal Raman Microscopy (CRM) as well as Electron Microprobe (EMP). The shell of L. elliptica has been previously described as being composed of aragonite exclusively. Now, CRM mapping reveals that three polymorphs of calcium carbonate – aragonite, calcite, and vaterite – are present in the chondrophore region of the examined individuals. Annual shell growth layers continue through aragonite and vaterite, suggesting simultaneous mineralization of both polymorphs. Spatially congruent EMP scans showed that the calcium carbonate polymorph affects the distribution of magnesium and strontium within the chondrophore. This is, to our knowledge, the first report of the coexistence of these three calcium carbonate polymorphs within the mineralized structures of a marine calcifying organism. Particularly the presence of vaterite is unexpected, but shows striking similarities to some fish otoliths. The strong effect of the calcium carbonate polymorph on trace element incorporation restrict the suitability of magnesium and strontium based proxies for the chondrophore area of L. elliptica.