Highly doped Poly (3,4-ethylenedioxythiophene) or PEDOT is a conductive polymer with a wide range of applications in energy conversion due to its ease of processing, optical properties and high conductivity. The latter is influenced by processing conditions, including formulation, annealing, and solvent treatment of the polymer, which also affects the polymer arrangement. Here we show that the analysis of the optical spectra of PEDOT domains reveals the nature and magnitude of the structural disorder in the material. In particular, the optical spectra of objects on individual domains can be used for the elucidation of the molecular disorder in oligomer arrangement which is a key factor affecting the conductivity. their conventional inorganic counterparts in a number of energy related applications [1], including photovoltaics [2,3], fuel cells [4,5] and low-cost and environmentally-safe thermoelectrics [6][7][8][9].A central feature of many of these devices is a transparent, flexible conductor layer. Among several materials employed for this layer, materials based on poly(3,4-ethylenedioxythiophene) (PEDOT) stand out due to their high hole conductivity, chemical stability, and transparency to visible light [10]. PEDOT-based structures have been incorporated in touch screens, light-emitting diodes, and photovoltaic elements, to mention a few examples [11]. Though multiple experimental investigations have addressed the molecular organization of PEDOT-based materials, the microscopic electronic states that lead to high conductance and the interplay between these states, optical properties, and the material structure has yet to be definitively characterized. The main obstacle to elucidating this relationship is the strong structural disorder that appears on multiple length scales and is highly sensitive to the preparation procedure [10].In this work, we link the supramolecular packing of PEDOT with its optical absorption spectra. We argue that optical spectroscopy of PEDOT aggregates on a single domain level can be used for characterization of the microscopic electronic structure in the material that is a function of molecular disorder. Specifically, we show how disorder in two packing models, widely accepted for PEDOT aggregates, leads to a transition between J-and H-aggregation [12,13] reflected in optical spectra. Finally, we identify the degree of disorder potentially responsible for this transition and study the changes in localization of the bright and dark states, in order to better understand the character of the spectral peaks. As we show below, disorder tends to localized the states and bright states are more delocalized than the dark ones. As a model system, we focus on structures composed of multiply charged oligomers. This model matches the experimentally determined charge density in highly conducting PEDOT.A high-conductance regime is observed for p-doped PEDOT [16] when the injection of positive charges induces a structural relaxation effectively forming polaron and bipolaron states [17]. In this case...