Tartary buckwheat is an important medicinal and edible crop known for its significant health benefits to humans. While numerous Tartary buckwheat germplasm resources have been collected in China, the genetic diversity and core germplasm resources remain largely unclear. The aim of this work was to analyze the genetic variability and construct a core germplasm collection of Tartary buckwheat. Fifteen highly polymorphic SSR markers were used to investigate 659 Tartary buckwheat accessions. A total of 142 alleles were marked, with an average of 9.47 alleles per locus. Genetic variability analysis revealed that these collected accessions exhibit high genetic diversity and can be classified into seven subgroups. Among wild, landrace, and improved accessions, the wild accession showed the highest genetic diversity, while no significant genetic variation was observed between the landrace and improved accessions. Based on genetic diversity and population structure analyses, a core germplasm collection containing 165 accessions (47 wild, 92 landrace, and 26 improved) was constructed, ensuring high genetic diversity and good representation. This study not only highlighted the genetic differences among Tartary buckwheat accessions, but also provided insights into the population structure and the development of a core germplasm collection. It provided important references for the conservation of genetic diversity and the genetic improvement of Tartary buckwheat.