SophoraeFlavescentisRadix(SophoraflavescensAit.,SFR)andSophoraeTonkinensisRadixetRhizoma(S.tonkinensisGapnep.,STR)aretwocommonlyusedtraditionalChinesemedicinesfromSophora(Leguminosae)plants,whicharebelievedtopossesssimilarbioactivecomponentswithentirelydifferentclinicalapplications.InordertofindoutthecharacteristicchemicalconstituentspotentiallyleadingtotheuniquemedicinalpropertiesclaimedforeachofthetwocloselyrelatedTCMs,anHPLCfingerprintmethodwasdevelopedforanalysesofthealkaloidandflavonoidconstituentsofSFRandSTR,respectively,whichwerefurtherevaluatedandcomparedthroughsimilaritycalculationandhierarchicalclusteringanalysis(HCA).Theresultsfromthepresentstudyshowedthatthealkaloidfingerprintsofthetwoherbsweresimilar,withmanycomponentsco-existinginbothdrugsandvariousbatchesofsamplesfromdifferentspeciesbeingmixedtogetherintheHCAdendrogram.However,theirflavonoidconstituentsweretotallydifferentwithspecificfingerprintsbeingyieldedforeachherb,andfurtherHCAanalysisshowedthatthetestedsamplescouldalmostbeclearlypidedintotwogroupsbasedontheiroriginsofspecies.TheresultsfromthepresentstudyindicatedthattheflavonoidconstituentscouldserveasthedifferentiallydiagnosticconstituentsofSFRandSTRandmightpotentiallyattributedtotheirdistincttherapeuticeffects.