Barley leaf stripe is one of the most serious diseases affecting barley yield and quality. In order to determine the resistant differences of barley germplasm to Pyrenophora graminea and explore candidate markers associated with resistance to Pyrenophora graminea. In this study， we identified the genetic diversity and population structure of 137 barley germplasms by 97 SSR markers and combined them with the results of resistance identification for association analysis. The results showed that 18 accessions were identified to be immunity， 27 highly resistant， 28 resistant， 42 susceptible， and 22 highly susceptible by artificial inoculation with Pyrenophora graminea strain QWC. A total of 651 alleles were detected in 85 primer pairs， with an average of 7.57 alleles. The genetic diversity index ranged from 0.0401 to 0.8646， with an average value of 0.5799. Polymorphism information content 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. The 137 barley germplasms were divided into four subpopulations by Cluster analysis and population structure analysis. A total of seven markers significantly （P<0.05） were obtainted to be associated with barley resistance to Pyrenophora graminea based on the general linear model， with the explained rates ranging from 5.80% to 17.89%， EBmatc0039 had the highest explained rate. EBmac77 and MGB357 were significantly associated with resistance to barley leaf stripe（P<0.01）， the two markers' rate of phenotypic variation explained were 6.07% and 9.60% in General Linear Model. The results of this study can provide reference for barley resistance to Pyrenophora graminea breeding.