Neutral cyclosophoraoses (Cys) and highly sulfated cyclosophoraoses (HS-Cys) were successfully applied as chiral selectors with SDS for the separation of some chiral flavonoids in MEKC. HS-Cys were synthesized by the chemical modification of a family of neutral Cys isolated from a soil microorganism, Rhizobium meliloti 2011. Chiral catechin was separated with a resolution (R-s) of 0.754 by neutral Cys and SDS. In the case of isosakuranetin and neohesperidin, resolution (R-s) values of 1.483 and 1.306 were obtained with HS-Cys and SDS, respectively.