Magnetic resonance microscopy (MRM) is an imaging modality that allows for noninvasive acquisition of high-resolution images in intact opaque animals. The zebrafish (Danio rerio) is an important model organism for the study of vertebrate biology. However, optical in vivo studies in zebrafish are restricted to very early developmental stages due to the opacity of the juvenile and adult stages. Application of high resolution MRM has not yet been explored in adult zebrafish. In this study we applied and optimized high resolution MRM methods to examine anatomical structures noninvasively in adult zebrafish. Clear morphological proton images were obtained by T(2)-weighted spin echo and rapid acquisition with rapid acquisition with relaxation enhancement (RARE) sequences which revealed many anatomical details in the entire intact zebrafish at a magnetic field strength of 9.4 T. In addition, in vivo imaging of adult zebrafish revealed sufficient anatomical details. To our knowledge this is the first report of the application of high resolution MRM to study detailed anatomical structures in adult zebrafish.