Einkorn wheat (AA), as the basic species of wheat, has lost some loci of the A chromosome during the evolution of bread wheat. Evaluating the genetic diversity and disease resistance level of einkorn wheat has important theoretical significance and breeding value for common wheat breeding and genetic improvement. In our study, 15 pairs of SSR primers with clear bands and high polymorphism were used to analyze the genetic diversity of 170 einkorn wheat materials, and the current epidemic stripe rust physiological race CYR34 was inoculated for disease resistance evaluation. The results showed that 71 alleles were obtained by SSR analysis, and the average polymorphism information content of primers was 0.6540; Cluster analysis and population structure analysis showed that tested materials could be divided into two groups in whom the average genetic distance was 0.4732 and 0.5404, respectively; Evaluation of disease resistance 19 materials with better resistance were obtained, including 3 immunity, 2 near immunity, 1 high resistance and 13 medium resistance materials, accounting for 11.17 % of the tested materials; Four pairs of primers had a correlation with the resistance of einkorn wheat to stripe rust. In summary, einkorn wheat contains abundant allele variations and contains stripe rust resistance genes, which has the breeding potential to improve wheat resistance to stripe rust.