Abstract: The aim of this study was to analyze the proteomic whiskers of Non-Arctocephalus pusillus, Arctocephalus australis and Arctocephalus philippi by label-free quantitative technology, and to explore the relationship between the three species of fur seal. The total protein was extracted from the beard samples of fur seal, and then the protein concentration was determined, electrophoresis, enzymolysis and peptide desalting were performed. Then the samples were analyzed by chromatography and mass spectrometry, database search, correlation analysis and hierarchical cluster analysis, differential protein screening and GO enrichment analysis.The results suggested that no obvious expression difference in proteins of beards between Arctocephalus australis and Arctocephalus philippi was found, showing a strong correlation and uniform self-expression. However, Non-Arctocephalus pusillus was found significantly different from Arctocephalus australis and Arctocephalus philippi, showing a weak correlation and an uneven self-expression. It could be deduced that the Non-Arctocephalus pusillus could be a different species under the seal family, showing relatively significant genetic differences and a distant genetic relationship with Arctocephalus australis and Arctocephalus philippi, which were found having a closer genetic relationship and could be classified a different subspecies.