MicroRNAs (miRNAs) are small noncoding RNAs that are found in both animals and plants. miRNAs function as negative post-transcriptional regulators during plant development and in response to biotic and abiotic stresses. In present study, high-throughput DNA sequencing and alignments with sequences from microRNA database (miRBase), a microRNA database, were used to identify drought stress-related miRNAs. This method is useful for identifying miRNAs and determining their expression profiles when genomic sequences are not available. Three drought-induced miRNAs, stu-miR396, stu-miR156a, and stu-miR157a were identified in potato (Solanum tuberosum). Effects of drought stress on their expression profiles were demonstrated, and their target mRNAs were predicted.