So far, only five microsatellite markers have been developed in common buckwheat (Fagopyrum esculentum). The purpose of the present study was to develop a larger number of microsatellite markers in common buckwheat. By sequencing 2785 clones from the libraries, which were enriched for (CT)n and (GT)n repeats using magnetic particles, it was shown that 1483 clones contained microsatellites, of which 352 had unique sequences. Primer pairs were designed for 237 of the microsatellite loci, of which 180 primer pairs each amplified PCR products. Fifty-four primer pairs that each amplified a clear PCR product of the expected size were evaluated for their ability to detect variations in common buckwheat populations and to be utilized in seven related Fagopyrum species. Forty-eight (88.9%) out of the 54 microsatellite markers tested were found to be highly variable (the average number of alleles was 12.2 and the average polymorphism information content (PIC) was 0.79) in a population of cultivated buckwheat. This PIC value was comparatively large when compared with the average values for microsatellite markers reported for other crops. A high rate of successful amplification of common buckwheat microsatellite markers was observed in closely related species; in particular all the 54 loci were successfully amplified in the wild ancestor of cultivated common buckwheat. The microsatellite markers developed in the present study should contribute to the promotion of molecular breeding in common buckwheat.