The influence of the monomer’s isomeric structures on the optical, electrochemical, charge transporting properties and photovoltaic performance of donor-acceptor (D-A) conjugated polymers is demonstrated for the first time by studying two D-A copolymers consisting of the bis(3-octyloxy)phenyl)quinoxaline as the electron deficient unit and the two isomeric structures of thienothiophene (thieno[3,2-b]thiophene and thieno[2,3-b]thiophene) as the electron rich units. The drastic effect of incorporating two different isomeric structures on the polymer backbone of these copolymers, manifests on changes observed in their optical, electrochemical and charge transporting properties. On the contrary, the overall photovoltaic performance of the copolymers is similar, but distinct differences on the device photocurrents occur. These differences on the device photocurrents were attributed to morphology variations rather than the balanced mobility ratio. For further developments in the field, the isomeric structures of different functional monomers should be considered in the designing of new materials with even superior performance.