CE-based techniques with DAD and detection ESI-TOF-MS have been developed for the analysis of seven protoberberine alkaloids and one aporphinoid alkaloid in Huanglian (Rhizoma coptidis), a well-known traditional Chinese herbal medicine. one aqueous BGE and one nonaqueous BGE were developed for CE-DAD and CE-MS analyses, and the CEESI-TOF-MS conditions including nebulizer gas pressure, the sheath-liquid composition, its flow rate, etc. were optimized. Eight main alkaloids in R. coptidis could be separated with baseline resolution by CE-DAD with these two different BGEs, and identified by TOF-MS analysis. Moreover, three major alkaloids (berberine, palmatine, and jatrorrhizine) could be quantified accurately by CE-DAD and CE-MS with the BGE system consisting of 50:50 v/v water and ACN containing 50 mM ammonium acetate at pH 6.8. Both techniques provided similar LODs and could be applied with confidence within similar linear dynamic range. However, reproducibility and speed of analysis were better using CE-DAD. When the CE technique was compared with the RP-H PLC method, the CE-DAD and CE-MS methods provided greater efficiency and faster analysis speed, i.e., achieving baseline resolution for all the eight main basic compounds in less than 14 min. The CE method, as a viable alternative to HPLC, is suitable for use as a routine procedure for the rapid identification and quantification of basic compounds in herbal or natural product applications.