The methanol extracts of 132 herbal medicines were screened for the inhibitory activity against heparinase enzyme from Flavobacterium heparinum. Eleven medicinal plants, Amomum xanthiodides, Agrimonia pilosa, Paeonia lactiflora, Rubia cordifolia, Sanguisorba officinalis, Torrega grandis, Morus alba, Gleditsia sinensis, Crataegus pinnatifida, Cornus officinalis, Paeonia japonica showed potent inhibition on heparinase activity. The active substituents of those herbal medicine could be extracted into butanol fraction and the inhibitory compounds of Morus alba are now isolating.