The metastable calcium carbonate polymorph vaterite has recently been found to occur commonly in freshwater cultured pearls from Japan and China. Organic pigment molecules in these vaterite regions of freshwater cultured pearls were analysed by resonance and near-resonance micro-Raman spectroscopy, in single spectra and in mapping modes and are compared with their aragonitic counterparts. Four different excitation wavelengths (487.9, 514.5, 532.2 and 632.8 nm) were used, resulting in differential increase of resolution for the pigments. Although vaterite areas were always lightly coloured (light yellow, light brown or white), ten different pigments were identified and a single colour is formed by a combination of three and up to nine polyenes of different lengths. The molecules were identified as unmethylated polyenes with effective chain lengths between 8 and 12 conjugated double bonds and FWHMs of 10 ± 2 cm-1. Additionally, and for the first time in pearls, methylated polyenes were detected together with unmethylated pigments in aragonite. Polyenes with chain lengths shorter than 8 or longer than 12 were not found in vaterite, whereas both shorter and longer pigment chains were observed in aragonite from the same pearls. Pigments have lower concentrations in vaterite and are distributed more homogeneously, while they have higher concentrations in aragonite and are arranged along the annual growth lines of the pearls.