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Electro-optical neural interface technologies provide great potential and versatility in neuroscience research. High temporal resolution of electrical neural recording and high spatial resolution of optical neural interfacing such as calcium imaging or optogenetics complimentarily benefit the way information is accessed from neuronal networks. To develop a hybrid neural interface platform, it is necessary to build transparent, soft, flexible microelectrode arrays (MEAs) capable of measuring electrical signals without light-induced artifacts. In this work, flexible and transparent ultrathin (<10 nm) gold MEAs are developed using a biocompatible polyelectrolyte multilayer (PEM) metallic film nucleation-inducing seed layer. With the polymer seed layer, the thermally evaporated ultrathin gold film shows good conductivity while providing high optical transmittance and excellent mechanical flexibility. In addition, strong electrostatic interaction via the PEM alters the electrode-electrolyte interfaces, thereby reducing the electrode impedance and baseline noise level. With a simple modification of the fabrication process of the MEA using biocompatible materials, both excellent transmittance, and electrochemical interface characteristics are achieved, which is promising for efficient electro-optical neural interfaces.