The invention discloses a recombinant hirudin encoding gene and the application. A nucleotide sequence is displayed in a 7-459th position from 5'end of a sequence 2 in a sequence table. The invention also discloses a recombinant expression vector and the recombinant expression vector contains the hirudin encoding gene. Recombinant bacterium can be obtained through introducing the recombinant expression vector in hansenulapolymorpha. The recombinant bacterium can produce recombinant hirudin with high level and the recombinant hirudin which is produced has high anticoagulation ration activity. The recombinant hirudin which is produced can prepare general anticoagulant of blood or plasma.