Phenolic acids have been focused on quite extensively in food science research for their antioxidative effect. In this study, the genotypic difference and genetic control in phenolic acids, and their correlation with malt quality were investigated in barley. Ferulic acid (FA) and p-coumaric acid (p-CA) were identified as two main phenolic acids, showing wide variations among 68 barley genotypes. The mean content of FA and p-CA were 2.15 μg g-1 and 1.10 μg g-1 in grains, and were 4.07 μg g-1 and 1.44 μg g-1 in malt, respectively. After malting, FA and p-CA increased significantly in 55 and 37 genotypes, but reduced in 2 and 14 genotypes, respectively. Both malt FA and p-CA were positively correlated with soluble N content and Kolbach index, and negatively correlated with malt extract and viscosity. The results indicated that the effect of malting on the change of individual phenolic acid is genotype-independent. Association mapping identified that 8 markers on Chromosomes 1H, 2H, 4H and 7H are associated with grain p-CA and 4 markers on Chromosomes 3H and 7H are linked with grain FA. However, only a single marker on Chromosome 3H was found to be associated with malt FA. Moreover, a lack of overlapping markers between grain and malt indicated the genetic diversity of phenolic acids in barley grain and malt. Our results strengthen the understanding of phenolic acids in barley and their responses to the malting process.