Polycondensation between the acceptor-donor monomer combination of squaric acid with 1-dodecyl- and 3-dodecylpyrroles provided conjugated macromolecules having two types of isomeric repeating units, depending upon the reaction conditions employed. Under azeotropic distillation using the 1-butanol-benzene solvent mixture (route A), the most preferred 1,3-zwitterionic repeating units were mostly formed, whereas in DMSO-acetic acid solvent under room temperature (route B), considerable amounts of the isomeric 1,2-diketonic repeating units were also formed along with the zwitterionic repeating units. Evidence for the structural differences of the polycondensation products obtained by routes A and B could be obtained from the detailed IR spectral analysis and studies of their physical properties such as solubility, molecular weight, optical absorption, solvatochromism, and conducting properties. The solubilities and the molecular weights of the polycondensation products having 1,2-diketonic repeating units obtained by route B were significantly enhanced when compared to those obtained as per route A. The UV-vis spectral and solvatochromic properties of the polymers obtained by routes A and B showed distinct differences, which were in accordance with their proposed structures. The electrical conductivities of the polymers obtained from 3-dodecylpyrrole and squaric acid by route B showed better values over polymers obtained through route A.