Self-assembled structures formed by perfluoropolyether (PFPE) carboxylates with hydrophobic chain terminated by Cl-C3F6O, and either sodium or ammonium counterions, have been explored in aqueous binary systems. The focus is on the different counterion-specific micelles and liquid crystals formed. These have been detected and characterized via optical microscopy, SAXS, and NMR. All Cl-PFPE surfactants form lamellar and cubic liquid crystals independently of chain length and counterion. Nonspherical micelles for the shortest PFPE chain surfactants and anomalous swelling of the lamellar phases for almost all surfactants were ascertained.