Isolation and mapping of genome-wide resistance (R) gene analogs (RGAs) is of importance in identifying candidate(s) for a particular resistance gene/QTL. Here we reported our result in mapping totally 228 genome-wide RGAs in maize. By developing RGA-tagged markers and subsequent genotyping a population consisting of 294 recombinant inbred lines (RILs), 67 RGAs were genetically mapped on maize genome. Meanwhile, in silico mapping was conducted to anchor 113 RGAs by comparing all 228 RGAs to those anchored EST and BAC/BAC-end sequences via tblastx search (E-value < 10-20). All RGAs from different mapping efforts were integrated into the existing SSR linkage map. After accounting for redundancy, the resultant RGA linkage map was composed of 153 RGAs that were mapped onto 172 loci on maize genome, and the mapped RGAs accounted for approximate three quarters of the genome-wide RGAs in maize. The extensive co-localizations were observed between mapped RGAs and resistance gene/QTL loci, implying the usefulness of this RGA linkage map in R gene cloning via candidate gene approach.