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The proteins of different faction of cowpea [Vigna unguiculata (L.) Walp] were fractionated by capillary electrophoresis (CE). The extracting solvent system was one of the most critical factors in the optimization exercise. To improve reproducibility, seed samples needed to be defatted with chloroform/methanol (V∶V＝2∶1) as preferred prior to protein extraction. Proteins were extracted from seeds, leaves and flowers with 50% aqueous 1-propanol and separated on a 50 µm×20 cm fused silica capillary column using a UV detector at 200 nm. Separation was conducted at constant voltage (10 kV, 40 ℃), using iminodiacetic acid (pH 2.5) containing 0.05% hydroxypropylmethylcellulose (HPMC) and 20% acetonitile. The results showed that proteins extracted from all fraction of cowpea were successfully separated by CE in less than 20 min. Seed extracts provided the greatest number of eluted protein peaks, followed by flower and leaf, respectively. The seed-protein extracts provided unique CE patterns for different varieties; hence the seed was the tissue chosen as being most suitable for variety identification. As a result, an optimized procedure was developed to provide rapid identification of cowpea varieties, based on capillary electrophoregram patterns.