Multimodal imaging combining optoacoustic tomography (OAT) with magnetic resonance imaging (MRI) enables spatiotemporal resolution complementarity, improves accurate quantification, and thus yields more insights into physiology and pathophysiology. However, only manual landmark based coregistration of OAT-MRI has been used so far. We developed a toolbox (RegOA), which frames an automated registration pipeline to align OAT with high-field MR images based on mutual information. We assessed the performance of the registration method using images acquired on one phantom with fiducial markers and in vivo/ex vivo data of mouse heads/brain. The accuracy and robustness of the registration are improved using a two-step registration method with preprocessing of OAT and MRI data. The major advantages of our approach are minimal user input and quantitative assessment of the registration error. The registration with MR and standard reference atlas enables regional information extraction, facilitating the accurate, objective, and rapid analysis of large groups of rodent OAT and MR images.