In spite of high morphological diversity, cultivated peanut (Arachis hypogaea) has low DNA polymorphism. This has hindered advances in peanut genetics and is a limitation for improvement of some crop traits. Due to their high genetic diversity and adaptation to a range of environments, wild relatives of peanut (Arachis spp.) constitute a rich source of allele diversity for resistance to abiotic stresses. In this study, the transcriptome of A. duranensis and A. magna, wild AA and BB diploid species, respectively, under gradual water stress was analyzed. For this, four cDNA libraries were constructed from leaf and root tissues collected from water-stressed and well-watered plants from both species. A total of 21,714 Unigenes from A. duranensis stressed and control material was obtained after clustering and assembly of Roche/454 reads, and 249 sequences from A. magna SSH libraries by Sanger sequencing. In silico analysis revealed that several genes were significantly up- or down-regulated in the stressed conditions. Differentially expressed candidate genes related to abiotic stress were selected for validation through RT-qPCR. The transcription profiles for two of them (expansin and nitrilase) showed high levels of differential expression in stressed plants, validating their involvement in drought response. This is, to date, the first report of new generation sequence analysis of wild Arachis transcriptomes under abiotic stress. The information produced in this study is a valuable resource for gene identification, characterization of new wild alleles, and molecular marker development.