Barley leaf stripe is one of the most serious diseases in barley. In order to determine the genetic differences of barley germplasm resistant barley leaf stripe and explore candidate markers associated with resistant to barley leaf stripe resistance genes. In this study, we identifited the genetic diversity and population structure of 137 barley germplasms by 97 pairs of SSR markers and combined them with the results of resistance identification for association analysis. The results showed that 18 accessions were identified to be complete resistance (no diseased symptoms), 27 highly resistant, 28 resistant, 42 susceptible, and 22 highly susceptible by artificial inoculation with QWC of Pyrenophora graminea. 651 alleles were detected in 85 primer pairs, with an average of 7.57 alleles detected per primer. The genetic diversity index ranged from 0.0401 to 0.8646, with an average value of 0.5799. PIC ranged from 0.0393 to 0.8498, and the average was 0.5155, the genetic distances ranged from 0.1021 to 0.4807, with an average of 0.2774, indicating the overall relationship is relatively distant. The 137 barley germplasms were divided into four categories by Cluster analysis and population structure analysis, each including 30, 16, 15,76 materials. A total of seven markers significantly (P<0.05) associated with barley leaf stripe resistance were obtained based on the general linear modelling method, with the explained rates ranging from 5.8 % to 17.89 %. The marker with the highest explained rate was EBmatc0039 and the one with the lowest explained rate was Bmag603. The results of this study can provide reference for Pyrenophora graminea resistance in breeding barley.