The winged pearl oyster, Pteria penguin, is a widely distributed and economically important bivalve with unique and primitive byssus. The byssogensis of this species is largely unknown. Here we report the lable free quantification analysis on different tissues of P. penguin.Through the analysis, we found that the process of byssogenesis requires ATP to provide energy among the differential proteins; and seven (Tenascin-X, laminin, papilin, fibrillin-1, spondin, protease inhibitors and Mucins) of the 31 proteins identified in the byssus were derived from ECM. Functions of extracellular matrix proteins can be correlated with the formation and the nature of the byssus.