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A large set of potential microsatellites markers covering the entire genome are required for genetic diversity, mapping and functional genomics studies. In this study, a total of 37,572 microsatellites with frequency of 83.25 microsatellites per Mb were mined in the recently sequenced Fagopyrum tataricum. Among these 37,572 microsatellites, most of the microsatellites were di-nucleotide (26,196, 69.72%) and AT/TA repeat motifs were the most abundant (24,742, 65.85%). A total of 26,549 microsatellite markers were designed from the flanking sequences of 37,572 microsatellites and 2643 (9.96%) were genic microsatellite markers. All of these newly-developed microsatellite markers were physically anchored to the eight chromosomes of F. tataricum and the first and high-density physical map was constructed with an average marker density of 58.82 markers per Mb. Amplification efficiency and experimental evaluation of the newly-developed microsatellite markers assessed with 440 markers randomly selected in F. tataricum, showed that these microsatellite markers are highly effective and valuable. The large number of new microsatellite markers and their location on the physical map provided a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in Fagopyrum species. [ABSTRACT FROM AUTHOR]