The soluble organic matrices were extracted from carbonated shells of molluscs and a Scleractinia. The composition was analysed with UV spectrometry, HPLC with a dual detection and 2D electrophoresis. Few data are available on such components. However, the obtained results confirm the previous data: quantities but also properties of the matrices are characteristic of the taxa. Proteins/sugars ratios, molecular weights and acidities differ in all the studied samples. The diagenetic changes are different for different species. In a multilayered shell, each layer has a particular diagenetic evolution. Thus, some biases are induced in the faunal statistics used in palaeoecological studies. After the death of the animal, the rates of degradation of the skeletons are different. The soluble organic matrices are more or less rapidly dispersed in sea water, depending on the resistance of the skeletons. From this point of view, fragile shells contribute largely to the organic composition changes of surrounding water. The faunal composition and the biochemical characteristics of the skeletons are important for the evolution of the marine environment. Their soluble organic matrices are dispersed in the water and sediments, and their strong acidity plays a major role in the precipitation of carbonates. Moreover, these invisible matrices are permanently recycled in sedimentary processes.