Jerusalem artichoke (JA) (Helianthus tuberosus L.) is a drought-resistant species. Through analyzing the transcriptomic data of JA, WRKY transcription factor genes closely related to drought stress response of JA were screened and analyzed, laying a theoretical foundation for clarifying the function of WRKY family genes of JA. Bioinformatics methods were applied to analyze the physicochemical properties, conserved domains, tertiary protein structures of WRKY gene family members in JA and their phylogenetic relationships with other species. RT-qPCR was used to detect the relative expression levels of WRKY genes in the seeds, roots, stems, leaves, petals and tubers under drought stress, and the transcription levels of WRKY gene family members in JA. A total of 74 WRKY genes were identified in JA leaves, with the sequence length ranging from 510 to 2 040 bp. The detected motif lengths ranged from 25 to 50 bases. Phylogenetic tree analysis showed that the most of the HtWRKY genes clustered with other WRKY genes. The results of tissue-specific expression analysis showed that the relative expressions of HtWRKY genes were higher in petals and tubers, and the drought-induced expression analysis showed that 20 and 19 HtWRKY genes were up-regulated in the leaves and roots of JA, respectively. HtWRKY is involved in the process against drought stress [ABSTRACT FROM AUTHOR]