Hyriopsis cumingii (Lea, Unionidae), a freshwater bivalve species widely distributed in China and commercially exploited for freshwater pearl production, was chosen as the reference model to investigate the protein signature in the organic scaffold matching calcium carbonate crystallization mode. This study takes advantage of different calcium carbonate habits production by the organism: aragonite in shell and pearl and vaterite in alternative pearl formation. Amino acid global composition and proteomics analysis have been undertaken to study the amino acid imbalance with respect to biominerals and microstructures. Forty peptides sequences were obtained by proteomics, of which ten are shared by all the different samples, nine are laced with aragonite; another nine with vaterite and twelve are related to pearls. Bioinformatics analysis allowed the peptides to be matched to the deduced protein sequences from EST databases and allowed functional assignment (e.g. scaffolding, strain strength, chitin binding or carbonic anhydrase function) to the proteins found in the different materials. Such panel of motifs tailored in vaterite and aragonite habits produced in a freshwater mollusk gives food for thought about organic control of the biomineralization processes.