Abstract: A method for identification of semen Cuscutae, a traditional Chinese herb, was developed. The proteins in semen Cuscutae were extracted under acid or basic conditions and separated by high performance capillary electrophoresis. The electrophoretograms of acidic or basic extractants from Cuscuta chinensis Lam., Cuscuta australis R.Br. and Cuscuta japonica Choisy showed significant differences, which can be used to identify the three different semen Cuscutae. The results of the identification for 13 pharmacognosical samples agreed well with those of scanning electronic microscopy and tissue microanalysis.