Plant productivity is influenced by environmental conditions. Abiotic stresses limit yield potential in crops. Mn toxicity is an important constraint to crop production. In this study, whole genome association mapping was used in a spring barley population with 148 diverse genotypes for morphological traits underlying Mn stress. Association analysis between markers and phenotypic traits was performed with a mixed linear model (MLM with K+Q). A total of 39 significant markers were identified under both non stress and stress conditions. These markers were found on chromosomes 1H, 2H, 3H, 4H and 5H. Many of the associated markers were located in regions where QTL had previously been identified. Three significant markers on chromosomes 3H and 5H were associated with main spike length (MSL) and awn length (AL). Thus, it can be proved that MSL and AL have the same controller genomic regions. The results indicated that Mn tolerance was quantitatively inherited, and the detected QTLs may be useful for marker-assistant selection and identification of the genes controlling Mn tolerance in barley.