Plants must respond and adapt to abiotic stresses to survive in various environmental conditions. Plants have acquired various stress tolerance mechanisms, which are different processes involving physiological and biochemical changes that result in adaptive or morphological changes. Recent advances in genome-wide analyses have revealed complex regulatory networks that control global gene expression, protein modification, and metabolite composition. Genetic regulation and epigenetic regulation, including changes in nucleosome distribution, histone modification, DNA methylation, and npcRNAs (non-protein-coding RNA) play important roles in abiotic stress gene networks. Transcriptomics, metabolomics, bioinformatics, and high-through-put DNA sequencing have enabled active analyses of regulatory networks that control abiotic stress responses. Such analyses have markedly increased our understanding of global plant systems in responses and adaptation to stress conditions.