For the study, three species commonly occurring in the coastal waters of China, i.e. Babylonia areolates, Solen arcuatus and Penaeus monodon, are respectively selected from the Gastropoda and Bivalvia of mollusks and the Crustacea of arthropods and their shell matrix proteins are extracted and analyzed. The proteomics analysis by using liquid chromatography tandem mass spectrometry (LC-MS/MS) reveals that the given protein has significant species differences: ①rotein N66 (a kind of carbonic anhydrase) occurs commonly in Solen arcuatus, but not in Babylonia areolates and Penaeus monodon. revealing that the protein N66 has the specificity, which may have important reference significance in species identification in the future; ②uticle proteins AM1199 and CP14.6 are generally found in the epidermal structure of Penaeus monodon , and not detected in Babylonia areolates and Solen arcuatus; ③emocyanin can be identified in the shell matrix proteins of all the three animals, revealing its important role in the shell formation and growth of different species. This study can provide a foundation for the identification of shell matrix proteins in mollusk or arthropod shells and also an important reference for exploring the biomineralization process in different species.