Heparinase is produced by growing the bacterium, Flavobacterium heparinum in an improved defined medium consisting of a carbon source, two or more amino acids and several salts in the absence of protein. The carbon source concentration is specifically kept below a certain level to promote improved heparinase production. The sulfate source concentration is also specifically kept below a certain level to promote improved heparinase synthesis. Heparinase can be produced in this medium with or without the addition of an inducer compound.