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The role of <i>bHLH</i> transcription factors in plant response to abiotic stress and regulation of flavonoid metabolism is well documented. However, to date, the <i>bHLH</i> transcription factor family in <i>Iris domestica</i> remains unreported, impeding further research on flavonoid metabolism in this plant. To address this knowledge gap, we employed bioinformatics to identify 39 <i>IdbHLH</i> genes and characterised their phylogenetic relationships and gene expression patterns under both drought and copper stress conditions. Our evolutionary tree analysis classified the 39 <i>IdbHLHs</i> into 17 subfamilies. Expression pattern analysis revealed that different <i>IdbHLH</i> transcription factors had distinct expression trends in various organs, suggesting that they might be involved in diverse biological processes. We found that <i>IdbHLH36</i> was highly expressed in all organs (Transcripts Per Million (TPM) > 10), while only 12 <i>IdbHLH</i> genes in the rhizome and four in the root were significantly upregulated under drought stress. Of these, four genes (<i>IdbHLH05</i>, -<i>37</i>, -<i>38</i>, -<i>39</i>) were co-upregulated in both the rhizome and root, indicating their potential role in drought resistance. With regards to copper stress, we found that only 12 genes were upregulated. Further co-expression analysis revealed that most <i>bHLH</i> genes were significantly correlated with key enzyme genes involved in isoflavone biosynthesis. Thereinto, <i>IdbHLH06</i> showed a significant positive correlation with <i>IdC4H1</i> and <i>Id4CL1</i> (<i>p</i> < 0.05). Furthermore, a transient expression assay confirmed that the IdbHLH06 protein was localised in the nucleus. Our findings provide new insights into the molecular basis and regulatory mechanisms of <i>bHLH</i> transcription factors in isoflavone biosynthesis in <i>I. domestica</i>.