| Summary: | <i>Hibiscus hamabo</i> Siebold & Zuccarini (<i>H. hamabo</i>) is tolerant to salt and drought conditions, but the molecular mechanisms that underlie this stress tolerance remain unclear. In this study, the transcriptome of <i>H. hamabo</i> roots was investigated under NaCl or PEG treatment. A total of 20,513 and 27,516 significantly changed known genes at 6 h and 24 h, respectively, were detected between the salt or drought treatments and the control libraries. Among these, there were 3845 and 7430 overlapping genes under the two stresses at 6 h and 24 h, respectively. Based on the analysis of enriched KEGG pathways and clustering of expression patterns, the DEGs that were continuously up- or down-regulated under both salt and drought treatments were mainly enriched in MAPK signaling pathway, transcription factors, transporters and other pathways. The transcriptome expression profiles of <i>H. hamabo</i> provide a genetic resource for identifying common regulatory factors involved in responses to different abiotic stresses. In addition, the identified factors may be useful to developing genetic breeding strategies for the Malvaceae.
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