We compared three different methods, i.e. trichloroacetic acid/acetone precipitation (TCA), trichloroacetic acid precipitation (E-TCA), and phenol extraction (Phe), to determine their efficiency in extracting total proteins from Salicornia europaea L. by two-dimensional electrophoresis (2-DE) analysis. Generally, 579, 343, and 535 protein spots were generated by the three methods. The 2-DE gels of TCA and E-TCA showed strong horizontal streaks, while that of the Phe method had only a few faint streaks, which indicated effective removal of salt from the protein sample by the Phe method. Moreover, an optimized extraction buffer of the Phe method was capable of generating more protein spots and gave more clear background in the 2-DE map. Findings from this study are of great significance for developing effective protein extraction methods for other halophytes, and halophilic microorganisms.