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Stemphylium blight (caused by Stemphylium botryosum Wallr.) is one of the major diseases of lentil (Lens culinaris Medik.) in South Asia and North America. The objective of the study was to identify linkage map position of the genes conferring resistance to stemphylium blight and the markers linked to the genes for its utilization in marker‐assisted breeding. A population of 206 F7–derived recombinant inbred lines (RILs) was developed from a cross between ILL‐6002 (resistant) and ILL‐5888 (susceptible). The RILs were planted in disease‐screening plots at Ishurdi, Bangladesh in the 2006–2007 and 2008–2009 winter cropping seasons. Significant variation was detected among RILs for disease scores and frequency distributions suggested complex inheritance. An intraspecific linkage map was constructed that comprised 139 markers; 21 simple sequence repeats (SSR), 27 randomly amplified polymorphic DNA (RAPD), 89 sequence related amplified polymorphism (SRAP) markers and 2 morphological markers distributed over 14 linkage groups. One significant quantitative trait loci (QTL) was detected based on disease scores from the 2006–2007 experiment while three significant QTLs were detected from the 2008–2009 experiment. The QTL QLG480–81 was common in both years and accounted for 25.2 and 46.0% of the variation of disease scores in 2006–2007 and 2008–2009 experiments, respectively. Two SRAP markers, ME5XR10 and ME4XR16c, and one RAPD marker, UBC34, located on linkage group 4, were significantly associated with the QLG480–81 in both crop years. After validation, the more tightly linked ME4XR16c marker may be used for marker assisted selection for stemphylium blight resistance.