The characterization and identification of reproducible, co-dominant genetic markers for studying the population genetics of the soil fungus Rhizoctonia solani anastomosis group 3 (AG-3) has been challenging. For example, it often requires many months to amplify, clone, sequence, and validate potential candidate loci, which often results in the discovery of only a relatively small number of genetic markers (often less than 10). In addition, traditional approaches involving the amplification of genomic DNA with randomly selected microsatellite-based primers, also has met with limited success for identifying useful genetic markers in R. solani AG1-IA, AG-3, and AG-4. With the advent of the Rhizoctoina genome project, we were interested in characterizing and identifying potential microsatellite markers for the Rhizoctonia community. We used the bioinformatics tool Tandem Repeats Finder http://tandem.bu.edu/trf/trf.html to identify tandem repeats of microsatellite motifs ranging from 2 to 9 bases in length in the draft genome sequence of R. solani AG-3 strain Rhs 1AP. Listed below are 269 microsatellite sequences identified in the genome with their respective flanking sequences. Please feel free to use these sequences for developing and validating microsatellite-based primers and genetic markers to address research questions related to R. solani. Good luck!