The utility and versatility of carboxylic single-walled carbon nanotubes (c-SWNT) in capillary electrophoresis (CE) is demonstrated, using as model solutes homologues and structural isomers. In the case of homologues of caffeine and theobromine, distinct changes in the electrophoretic parameters occur at a critical concentration of c-SWNT in the run buffer. It is suggested that the c-SWNT of a definite concentration could form a network in the run buffer as a pseudostationary phase on the basis of the unique tubule structure, providing a different separation from sodium dodecyl sulfate (SDS) micelles. In the case of structural isomers of catechol and hydroquinone, differing from the homologues, it is mainly attributable to the functional groups on the c-SWNT that have an effect on the electrophoretic behaviors by forming intermolecular hydrogen bonding with analytes. Furthermore, aggregated c-SWNT serve as anticonvective media and minimize solute diffusion contributing to zone broadening. The presence of charged c-SWNT suppressed the electrodiffusion and decreased the adsorption between capillary wall and solutes, which led to better peak shapes of isomers.