Potato (S. tuberosum) is a highly heat-sensitive crop; a slight rise from optimal temperature can lead to drastic decline in tuber yield. Despite several advancements made in breeding for thermo-tolerant potato, molecular mechanisms governing thermo-tolerance is poorly understood. The first step towards understanding the thermo-tolerance mechanism is to identify the key genes involved in it. Here we used a yeast-based functional screening method to identify, characterize and classify potato genes with potentials to impart heat tolerance. We constructed two cDNA expression libraries from heat-stressed potato plants (35 °C) after 2 and 48 h of treatment. 95 potential candidate genes were identified based on enhanced ability of yeast cells over-expressing heterologous potato cDNA sequences to tolerate heat stress. Cross-resistance analysis of these heat-tolerant yeast clones to other abiotic stresses indicated that 20 genes were responsive to drought, 14 to salt and 11 to heat/drought/salt stresses. Comparison of 95 genes with reported whole potato transcriptome data showed that majority of them have varying expression patterns under heat, drought and salt stresses. The expression pattern was validated by analyzing the expression of 22 randomly selected genes under various stresses using qPCR. Gene ontology (GO) enrichment analysis of these 95 genes indicated that most of them are involved in various cellular metabolism, signal transduction, response to stress and protein folding, suggesting possible role of these genes in heat tolerance of potato. Genes identified from this study can be potential candidates for engineering heat tolerance as well as broad-spectrum abiotic stress tolerance of potato.