Isatis　indigotica　Fort.　(Chinese　woad)　has　been　widely　used　as　a　dye-　and　medicinal-plant　in　traditional　Chinese　medicine.　Although　I.　indigotica　has　been　cultivated　in　various　regions　across　China　in　recent　years,　its　innate　immunity　is　little　known.　In　this　study,　a　protein　with　MW　37.5　kDa　was　purified　from　the　extract　of　fresh　Isatidis　roots　by　SP-5PW　cationic　exchange　and　POROS　HP2　hydrophobic　interaction　chromatography.　The　N-terminal　amino　acid　sequence　of　the　purified　protein　was　subsequently　determined　as　T-D-L-C-H-K-D-P-K-N-T-L-L　by　Edman　degradation.　The　N-terminal　sequence　and　PG　inhibitory　activity　identified　the　purified　substance　as　a　polygalacturonase　inhibiting　protein.　This　purified　Isatidis　PGIP　with　a　specific　activity　of　7.64×104　U/mg　showed　strong　inhibitory　activity　against　160　U　of　Aspergillus　Niger　polygalacturonase.　Compared　with　PGIPs　from　guava　and　bean　pods,　Isatidis　PGIP　showed　very　poor　pH　and　heat　stabilities,　which　may　represent　the　different　need　of　plant　innate　immunity　between　plant　underground　and　aboveground　organs.