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This study investigates the response of lentil genotypes to Stemphylium blight disease over two cropping years, 2021 and 2022. In addition, this research aims to assess the marker-trait association between Stemphylium disease progress and the selected SSRs. Visual symptoms were assessed using Hashemi's disease scoring system, leading to the calculation of disease parameters such as Percent Disease Index (PDI) and Area Under Disease Progress Curve (AUDPC). The results revealed variations in disease progress among genotypes, with some exhibiting low disease indices, particularly genotype IC241072. Genetic diversity analysis using SSR markers identified 30 alleles and grouped genotypes into four clusters. Principal Coordinate Analysis (PCoA) confirmed the genetic distances among genotypes. Marker-trait association analysis linked the microsatellite locus LCSSR04_130362_118bp to Stemphylium blight resistance, supported by the identification of a TCP family transcription factor in close proximity. The validation of the association indicated a significant difference between resistant and susceptible alleles. This comprehensive approach combining field screening, genetic diversity analysis, and marker-trait associations provides valuable insights into the genetic basis of Stemphylium blight resistance in lentil genotypes, offering potential candidates for future breeding programs. [Display omitted] • Investigation of lentil genotype response to Stemphylium blight disease in year 2021 and 2022. • Marker-trait association assessment using SSRs for Stemphylium disease progress. • Disease progress higher in 2021, specific genotypes (IC241072, IC544556) identified. • Genetic diversity among 50 lentil genotypes revealed four clusters. • Marker allele (LCSSR04_130362_118bp) associated with AUDPC and potential role in disease resistance. [ABSTRACT FROM AUTHOR]