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Two genes, <i>HvSAP8</i> and <i>HvSAP16</i>, encoding Zinc-finger proteins, were identified earlier as active in barley plants. Based on bioinformatics and sequencing analysis, six SNPs were found in the promoter regions of <i>HvSAP8</i> and one in <i>HvSAP16</i>, among parents of two barley segregating populations, Granal × Baisheshek and Natali × Auksiniai-2. ASQ and Amplifluor markers were developed for <i>HvSAP8</i> and <i>HvSAP16</i>, one SNP in each gene, and in each of two populations, showing simple Mendelian segregation. Plants of F₆ selected breeding lines and parents were evaluated in a soil-based drought screen, revealing differential expression of <i>HvSAP8</i> and <i>HvSAP16</i> corresponding with the stress. After almost doubling expression during the early stages of stress, <i>HvSAP8</i> returned to pre-stress level or was strongly down-regulated in plants with Granal or Baisheshek genotypes, respectively. For <i>HvSAP16</i> under drought conditions, a high expression level was followed by either a return to original levels or strong down-regulation in plants with Natali or Auksiniai-2 genotypes, respectively. Grain yield in the same breeding lines and parents grown under moderate drought was strongly associated with their <i>HvSAP8</i> and <i>HvSAP16</i> genotypes. Additionally, Granal and Natali genotypes with specific alleles at <i>HvSAP8</i> and <i>HvSAP16</i> were associated with improved performance under drought via higher 1000 grain weight and more shoots per plant, respectively.