Tartary buckwheat has become a popular health food in China. In the current study, through selectively amplifying microsatellite-containing sequences，recombining the amplicons by redigestion and ligation, and constructing SSR loci library, an effective method of recombinant microsatellite ampli?cation was developed. With this method, we designed 500 pairs of primers, and tested in tartary buckwheat. The effectiveness of these SSR primers in tartary buckwheat is about 50%, the polymorphic rate is 10.8% and the average value of PIC is 0.3600. We analyzed the genetic diversity of core collection of tartary buckwheat with 28 SSR markers. A total of 85 alleles were identified, ranging from 2 ~ 5 with averaged 3 per locus. Shannon’s information indices of geographical variation were 0.3633 ~ 0.6671. The accessions from Yunnan, Sichuan and Tibet are not only abundant in genetic diversity but also have the close phylogenetic relationship. This further confirmed that tartary buckwheat originate in the Southwest of China. This study demonstrates that the recombinant microsatellite amplification method for development of SSR primers in tartary buckwheat would be very effective, and will contribute to the researches on genetic diversity analysis, identification of useful traits and marker-assistant breeding in tartary buckwheat.