We have constructed a BAC library for common buckwheat Fagopyrum esculentum Moench. The library includes 142,005 clones with an average insert size of approximately 76 kb, equivalent to approximately a 7 to approximately 8-fold coverage of the genome. Polymerase chain reaction based screening of the library with AGAMOUS and FLORICAULA/LEAFY primers, has identified 7 and 9 BACs, respectively, which are consistent with the genome coverage. This library represents the first large insert genomic library for F. esculentum and it can be served as a genetic resource facilitating agricultural, pharmacological, physiological, and evolutionary studies of the species. To demonstrate the utilization of the library for characterizing agriculturally valuable traits, we developed a sequence tagged site marker tightly linked to the dwarf E locus as well as to the self-incompatibility complex locus and screened the library to initiate positional cloning of the causative genes.