We constructed a restriction site associated DNA (RAD) marker microarray to facilitate rapid genetic mapping of zebrafish mutations. Using these microarrays with a bulk segregant approach, we localized previously unmapped mutations to genomic regions just a few centiMorgans in length. Furthermore, we developed an approach to assay individual RAD markers in pooled populations and refined one region. The RAD approach is highly effective for genetic mapping in zebrafish and is an attractive option for mapping in other organisms.