A　simple　method　was　established　to　determine　protoberberine　alkaloids　in　Cortex　Phellodendri　and　Rhizoma　Coptidis　based　on　an　acidic　potassium　permanganate　chemiluminescence　(CL)　system.　The　optimum　conditions　for　the　CL　reaction　between　protoberberine　alkaloids　and　potassium　permanganate　were　studied　in　detail.　Under　the　optimum　conditions,　the　linear　response　ranges　for　berberine,　palmatine　and　jatrorrhizine　were　0.038-7.27,　0.031-18.1　and　0.012-3.61　mu　g/mL　with　detection　limits　of　0.005,　0.004　and　0.0007　mu　g/mL,　respectively.　This　method　was　successfully　applied　to　determine　the　content　of　protoberberine　alkaloids　(calculated　using　berberine　as　an　index)　in　Cortex　Phellodendri　and　Rhizoma　Coptidis.　In　addition,　a　possible　mechanism　of　this　CL　reaction　was　proposed　on　the　basis　of　the　investigation　of　CL,　UV　and　fluorescent　spectra　of　protoberberine　alkaloids　in　acidic　solution　containing　potassium　permanganate.　Copyright　(C)　2009　John　Wiley　&　Sons,　Ltd.