Computer-controlled microscopes with digital image acquisition and analysis led to the creation of a new field, called Digital Microscopy. Digital Microscopy not only allows a certain degree of automation but also has brought new possibilities to microstructural characterization. One of these new and promising possibilities is Co- Site Microscopy, that links different kinds of information, obtained from different microscopy techniques. The present work presents the development and implementation of a Co-Site Microscopy methodology that combines images obtained by Reflected Light Microscopy (RLM) and Scanning Electron Microscopy (SEM). This methodology involves the whole sequence, from image acquisition at the microscopes to the analysis of the phases using Pattern Recognition techniques. An automatic registration procedure for the two kinds of images was developed, allowing the adjustment of magnification, translation, rotation, and pixel size, and the correction of local distortions. The methodology was tested with several mineral samples, aiming at the discrimination of phases that are not distinguishable with either RLM or SEM. The RLM-SEM Co-Site Microscopy technique was employed in the characterization of iron ore samples and the obtained results were compared to the traditional analysis by SEM.