The development of new analytical techniques for identifying endogenous peptides in a cell, organ, or organism (the peptidome) is an important work in the fields of peptidomics and proteomics. MS is currently employed as a powerful analytical technique in peptidomics. However, it has a limitation in the identification of peptides with the same amino acid composition but different sequences, as these peptides have the same molecular weights, and generate the same MS spectrum of molecular ions, when MS is used as the detection technique. Therefore, the development of peptide separation techniques like CE and LC coupled with MS is desirable. In this paper, a methodology for the separation of peptides with the same amino acid composition, but different sequences, by CE has been developed using two tripeptides, Gly-Ser-Phe and Gly-Phe-Ser, as a model sample. Excellent separation selectivity was achieved using the separation mode of MEKC. Separation behavior under different conditions and mechanism is discussed.