Drought stress during the seedling stage has a disastrous effect on the growth of maize. The purpose of this study was to assess the developed expression markers that are related to drought stress in maize. For the selection of expressed genes by drought stress, co-expression analysis was carried out using published microarray data of drought stress in maize (Zea mays L.) seedlings. Six consensus modules were based on 4,770 stress responsive genes differentially expressed in drought stress, and the royal blue module was chosen. Thirty genes were selected according to different expression patterns between susceptible and tolerant types. Drought stress treatments were performed on both Ki3 and Ki11. Ki3 and Ki11 are widely known drought-susceptible and -tolerant types, respectively. At first, the 30 selected genes were compared to Ki3 and Ki11 using qRT-PCR. The gene expression values of eight genes (BU050895, BF728598, CK827168, CO524848, AF457983, CF037152, AJ606944, and BG836522) were significantly tolerant types rather than susceptible types in the roots. After applying the eight above-mentioned genes to nine cultivars, a different pattern was detected between susceptible and tolerant types. The results of the present study will show the possibility of developing novel expression markers and the application for various maize varieties.