The invention discloses deep-sea bacterium keratinase, a coding gene thereof, a zymoprotein producing engineering strain and an application. The invention provides protease formed by an amino acid sequence shown in SEQ ID No. 2 or SEQ ID No. 5 or a derived protein with one or more substituted, deleted or added amino acids and keratinase activity and an encoding gene sequence thereof. A deep-sea bacterium keratinase gene kr0631 has a nucleotide sequence shown in a sequence list SEQ ID No. 1, and an encoded protease sequence is shown in SEQ ID No. 2. The protease has the characteristic of degrading keratin, and the ectoenzyme yield of a recombinase can be remarkably increased through combining a signal peptide sequence and a protease gene. The invention has extensive use in the aspect of treatment of waste refractory protein organics of environments.