Electrochemical oxidation of insoluble highly ordered bis(4-dimethylamino-2-dihydroxyphenyl)squaraine (1-1OHSQ) dye layers adsorbed on highly oriented pyrolytic graphite (HOPG) electrodes was studied in aqueous electrolytes. Staircase cyclic voltammetry obtained in chloride electrolytes revealed hysteresis characterized by large peak separations (100-200 mV) and sharp redox peaks (full width at half maximum (fwhm) 10-60 mV) the shape and potentials of which depended on electrolyte concentrations. Small stochastic reduction peaks were observed at more negative potentials that are associated with the reduction of small domains of the oxidized 1-1OHSQ layers. Peak potentials and peak shapes were also dependent on the identity of the electrolyte anion species. The results support a reaction scheme where electrolyte anions are incorporated into surface confined one-electron oxidized dye molecular layers. From the results of peak potential shifts: the preference for ion-pairing is estimated to be in the order of: I- > Br- > Cl-> SO42- approximate to ClO4- approximate to F-. Ex-situ STM observations were performed to reveal structural changes upon electrochemical oxidation of 1-1OHSQ layers in LiCl electrolytes. Two polymorphs with different angles of the long-axis of molecules to the directions of the molecular row were observed for the oxidized samples. Both polymorphs had larger packing densities compared to the reduced form of the dye.