We describe two novel methods to analyze the microstructure of mollusc shell layers in situ in shell sections. Living abalone, Haliotis rubra (Leach), were immersed in seawater baths to which manganese chloride tetrahydrate was added. Distinct cathodoluminescent marks were produced within shell layers formed during the immersion period. Electron and proton microprobe analysis of shell sections confirmed that concentrations of manganese ions within aragonitic and calcitic shell layers are associated with yellow-green and orange-red luminescence, respectively, which allows us to distinguish mineral types. Colored cathodoluminescent marks within shells show that the mineralization of aragonite and calcite may occur simultaneously in the prismatic layer, but also that mineralization under one area of the mantle may switch between polymorphs over short periods. Using cathodoluminescent marks, we show that Raman laser spectroscopy can distinguish mineralogical types in situ and that the dark nacreous layers, variously described as 'growth checks' or conchiolin layers, contain aragonite rather than calcite.