Potato (Solanum tuberosum) is the third most important crop and the most relevance dicot in human feeding. Water stress is the greatest limitation of crop production. In response to drought, the plant triggers strategies that involve morphological, physiological and biochemical changes, polygenic traits controlled by additive genes and often synergistic. We focused on the analysis of transcriptional profiling on genotypes of Solanum wild species: S. venturii and S. cardiophyllum that present contrasting behavior under water stress using cDNA microarray hybridizations. Solanum wild species are a rich source of novel genes for introduction into cultivated species to enhance drought tolerance. Bioinformatic analysis of expression data of Solanum wild species showed significant differences in transcriptional profiles. Differentially expressed genes vary not only in number but also in their temporal expression profiles. These differences between wild potato species suggest new ways to exploit the genetic variability of wild germplasm for crop breeding.