High-resolution microelectrodes made of transparent conducting materials are advantageous for electrophysiology recordings when used in combination with optogenetic stimulation or optical imaging. Existing transparent electrodes made of indium tin oxide (ITO), ultrathin metal, graphene, poly-(3, 4-ethylenedioxythiophene)/poly(styrenesulfonate) (PEDOT:PSS), gold nanomesh, or silver nanowire network present tradeoffs with optical transmittance, resistivity, mechanical flexibility, and biocompatibility. In this work, we designed and constructed a flexible, fully transparent microelectrode array using a PEDOT:PSS/ITO/Ag/ITO multilayer assembly. Nanometer-thick Ag provides high electrical conductivity while being transparent over a broad spectrum. ITO offers excellent transparency as well as chemical and biological stability to protect Ag from corrosion in the biological environments. PEDOT:PSS further reduces electrochemical impedance by increasing the active surface area with the same electrode size. The thickness of each layer of the multilayer assembly was optimized at a specific wavelength using admittance loci analysis to minimize the reflectance at the inhomogeneous material interfaces. As a proof of concept, an electrode array was designed to have two sub panels, each of which consisted of 16 microelectrodes on a 3x3 mm2 area, with various electrode diameters of 25 µm to 50 µm. The fabrication of such an array started from Parylene C deposition on a 3-inch silicon wafer. Photoresist (PR) was spun on the substrate and photolithographically patterned as a sacrificial mask. After that, ITO (20 nm), Ag (9.5 nm) and ITO (24 nm) thin films were sputtered consecutively in a radio-frequency (RF) magnetron sputtering system (Denton Explorer-14, Denton Vacuum, Inc), and then patterned using the liftoff process to form microelectrodes, interconnection wires, and contact pads. Next 2 μm Parylene C was deposited on the substrate as an insulating layer and selectively etched using oxygen plasma dry etching (RIE-1701 plasma system, Nordson March, Inc) to expose the recording sites and contact pads. After that, another PR mask was patterned to expose only the microelectrode sites followed by coating diluted 0.55% PEDOT:PSS. Finally, PR was rinsed off with acetone, IPA and DI water to remove unwanted PEDOT:PSS, leaving PEDOT:PSS only on top of the ITO-Ag-ITO microelectrodes.The optical, electrical, electrochemical, and mechanical properties of the PEDOT:PSS-ITO-Ag-ITO multilayer assembly was characterized using various experimental methods. In particular, a Filmetrics thin film analyzer was utilized to measure the transmittance of thin films in a wavelength range of 300 nm - 800 nm (F20-UVX, Filmetrics, Inc) and a four-point probe (SRM-232, Bridge Technology, Inc) analyzer was used to measure the sheet resistances of the samples. Compared to a single ITO film of the same thickness, the PEDOT:PSS/ITO/Ag/ITO assembly exhibits a combination of high broad-band transmission (>80%) and significantly improved conductivity. Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) analyses demonstrated the significantly enhanced electrical impedance of the multilayer film by 91.85%. The electrochemical impedance of the films remained stable after 12 weeks of storage in room temperature air, with less than 12% change. Meanwhile, peel-off tests verified the excellent adhesion of the ITO-Ag-ITO assembly on the Parylene C substrate, and bending test results demonstrated the mechanical flexibility of the combined thin films over a large surface area. In addition, the noise performance of the transparent microelectrodes was analyzed under exposure to optical illumination of various wavelengths, confirming the negligible photon-induced artifacts suitable for electrophysiology recording in combination with optical imaging or stimulation. The optical transparency of the microelectrode array was further demonstrated under both the fluorescent and bright-field illumination conditions. Finally, the ability to use the transparent microelectrodes for recording neurophysiology and electrocardiography signals was demonstrated in vivo using rat models or in vitro using heart organoids.