EKC methods for the enantiomeric resolutions of melatoninergic ligands were developed using anionic CDs (highly S-alpha-CD, highly S-beta-CD, and highly S-gamma-CD) as chiral selectors at acidic pH 2.5. The optimization of the various operational parameters (nature and concentration of the CD, phosphate buffer concentration, addition of organic modifiers in the BGE, and temperature) allows baseline enantioresolutions (superior to 2) in short analysis times (inferior to 7 min) for all studied analytes. Some analytical characteristics of the optimal method were then studied for each analyte: repeatability, linearity, and LOD and LOQ. Lastly, determination of the apparent binding constants for the 18 complexes formed between the six analytes and the three CDs led us to rationalize the complexation mechanisms.