To establish and compare the total protein fingerprints and the fractional fingerprints of Bombyx Batryticatus from Yunnan and Sichuan,and to discover the differentially expressed protein molecules,and to identify and analyze them by mass spectrum and bioinformatics,to explore the feasibility of its application in geographical origin identification.The total acid-soluble,alkali-soluble,water-soluble and alcohol-soluble proteins of the two kinds of Bombyx mori were extracted,and they were fractional precipitated with acetone.The SDS-PAGE fingerprints of the obtained samples were compared and analyzed.The differential bands were analyzed by LC-MS/MS,and the bioinformatics analysis was conducted after database retrieval.The similarity of the total protein fingerprints of these two kinds of Bombyx Batryticatus was very high,so it is difficult to use for geographical origin identification of this Chinese medicinal material.The fractional fingerprints of these two kinds of Bombyx Batryticatus were relatively different,which is expected to be used for the identification of its geographical origin.According to the difference of fractional fingerprints,273 proteins including chymotrypsin inhibitor,trypsin inhibitor,fumarylacetoacetate hydrolase domain-containing protein and lipase domain-containing protein were identified.There were significant differences in protein composition and fractional fingerprints between Bombyx Batryticatus from Yunnan and Sichuan,which were expected to be used as molecular basis for geographical origin identification.The construction of fractional fingerprints of alcohol-soluble proteins can provide more abundant information and better resolution.The fractional fingerprint technology has the advantages of simplicity and high resolution,which provides a methodological idea for the identification of other Chinese medicinal materials.