<p>Tartary buckwheat landraces from Yunnan represent a crucial genetic reservoir for modern breeding. Simple Sequence Repeat (SSR) and Inter Simple Sequence Repeat (ISSR) markers were utilized to evaluate the genetic diversity of 33 tartary buckwheat accessions that were collected from 22 counties in 11 prefectures in Yunnan. Five ISSR primers amplified 88 bands, of which 74 (84.30%) were polymorphic, while seven SSR primers amplified 184 bands, of which 178 (96.74%) were polymorphic. Nei’s gene diversity (H = 0.43) and Shannon’s information index (I = 0.62) generated using the SSR primers were higher than those with ISSR primers (H = 0.41, I = 0.58), indicating that the SSR system is more effective than the ISSR system in evaluating the genetic diversity of a variety of <i>F. tataricum</i> accessions. The mean genetic similarities were 0.76, 0.73, and 0.75, as assessed using SSR, ISSR, and combined SSR/ISSR, respectively. The results indicate that the genetic diversity among <i>F. tataricum</i> accessions is very high. We clustered the 33 <i>F. tataricum</i> accessions into two groups on the basis of the phylogenetic trees constructed based on the unweighted pair group method with arithmetic mean (UPGMA). Accessions 4 (Deqin, Diqing) and 28 (Weixi, Diqing) are consistently identified as a distinct genetic cluster by all marker methods. The results of principal coordinate analysis (PCoA) further corroborated the UPGMA clustering. This study on the diversity of tartary buckwheat landraces in Yunnan will provide a foundation for subsequent research on the genetic diversity of tartary buckwheat landraces in China and globally, as well as for improved exploitation, conservation, and management of tartary buckwheat resources.</p>