Plants growing in natural habitats are exposed to multiple environmental stresses resulting from abiotic factors such as heat, drought, and cold, which have a significant impact on cultivated potato. We have evaluated in two Solanum tuberosum varieties, Soprano and Kondor, the adaptation to different abiotic stresses as heat, cold, and drought. For this purpose plants of both varieties were stressed, and when they showed symptoms, RNA extraction was carried out and a cDNA library for each sample was constructed. The objective of this study was to detect and analyse the genes involved in the responses to abiotic stresses in potato. The assay generated transcriptome sequences from both varieties, and a total of 5.579.655 reads and 8420 putative candidate genes were generated. 4.027 of the candidate genes were polymorphic and presented a different number of patterns defined by a varying number of SNPs. Many of the generated candidate genes showed differential expression, since the candidate gene was present in the stressed plant, but not in the control plant. The application of this methodology allows us to detect numerous candidate genes or specific alleles/allele combinations, which are differentially expressed in specific samples after the application of different abiotic stresses. This will be useful to identify superior alleles which can be used in Marker Assisted Selection for resistance and tolerance to abiotic stresses.