Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.Heat, cold, salinity or drought, constitute abiotic stress conditions that are sub-optimal for plant growth 1 . Plants have evolved complex signaling transduction pathways to perceive and respond to environmental changes. These are initiated from multiple sites within the cell and terminate in the nucleus, influencing gene expression via networks of transcription factors (TFs), allowing plants to regulate their energy expenditure and growth as they mount an adaptive response to the stress 2,3 . While many components of these pathways have been elucidated, much remains unclear about the underlying mechanism of transcriptional regulation. Phytohormones, including jasmonic acid (JA), ethylene (ET), salicylic acid (SA) and abscisic acid (ABA), play key roles in the regulation of stress responses 4,5 . Recent evidence indicates extensive crosstalk between these pathways and those of growth-regulating hormones auxin, brassinosteroid (BR), cytokinins and gibberellic acid (GA). Signals mediated by reactive oxygen species (ROS), Ca 2+ and metabolites also play critical roles in abiotic stress responses, relaying the status of the chloroplast and mitochondria through retrograde signaling to the nucleus to influence gene expression 6,7 .Transcriptional control of abiotic stress responses is orchestrated through a network of more than 1,500 TFs in Arabidopsis 8,9 . Transcriptional regulation in eukaryotic cells requires interplay of various factors; including RNA polymerase II (pol II), general transcription factors (GTFs), transcriptional activators/repressors, and co-regulators, such as Mediator 10 . Mediator is a large multi-subunit...