As pomegranate ( Punica granatum Linn.) processing is fast growing, the usage of pomegranate processing wastes containing seeds has been receiving great attention. The protein component accounts for 100–130 g/kg of the seeds in weight. However, so far, there is no information on the composition and function of the pomegranate seed proteins. In this study, a global view of water-soluble non-storage proteins isolated from mature pomegranate seeds were studied using two-dimensional polyacrylamide gel electrophoresis coupled with liquid chromatography–tandem mass spectrometry. With the two-dimensional polyacrylamide gel electrophoresis approach, over 120 protein spots were resolved, of which 7 abundant protein spots showing low molecular mass were identified. These identified proteins may be linked to seed development and metabolism, but more importantly, the occurrence of these proteins provides the possibility of conversion the pomegranate processing wastes into useful products or raw material for food industry.