Abstract: Core primers are important in genetic diversity analysis, cultivar identification, and fingerprinting construction. In this study, 91 pairs of EST-SSR primers were screened using 35 registered tartary buckwheat cultivars, with 50 primers showing polymorphism. Based on the polymorphism information content (PIC) and discrimination power (DP) results, a core set of six SSR primers (SSR9007, SSR6873, SSR7642, SSR2234, SSR6789, and SSR68216) were further selected to construct fingerprinting of the 35 cultivars, with alleles amplified by each pair of primers ranging from 2 to 4 and PIC values ranging from 0.60 to 0.78. The UPGMA cluster analysis showed that the genetic similarity of the 35 cultivars varied from 0.50 to 0.99. The cultivars were divided into four groups based on a genetic similarity of 0.60, with 54.3% remaining clustered together, indicating a close genetic relationship and narrow genetic basis. The genetic relationship was in accordance with their breeding history, but was not affected by their geographic differences.