<p>Ultra-flexible electrodes, due to their superior biocompatibility, are likely to lead the future of neuroprosthetics. However, identifying the precise positions of implanted high-density ultra-flexible electrodes in the brain for accurately assigning neural signals to specific structures remains a major challenge. To address this, we developed magnetic resonance identification (MRID)-tags. Each ultra-flexible electrode bundle carries an MRID-tag with unique barcode patterns visible in MRI (MRI-barcodes) for identification of the bundle. Individual bars in MRI-barcodes allow an accurate 3D reconstruction of the ultra-flexible electrode bundle’s trajectory in the brain and determine the anatomical positions of individual electrodes. We generate the MRI-barcodes by patterning superparamagnetic iron-oxide nanoparticles into electrode fibers (10&#xa0;µm²) with dot-matrix nanoparticle coating technique. We chronically tested MRID-tagged ultra-flexible electrodes in vivo in the dorsal hippocampus of freely-moving rats, where distinct electrophysiological landmarks validated our electrode localization results. We were able to localize individual electrodes with a mean accuracy of 95 μm. MRID-tagged ultra-flexible electrodes demonstrated high long-term recording stability with mean single-unit signal-to-noise ratios as high as 20.</p>