Introduction: Flavonoids in the leaves of Blumea balsamifera (L.) DC. have prominent anti-inflammatory and antioxidant activities, conferring high medicinal value to the plant. However, the key genes governing flavonoid biosynthesis and environmental adaptability in this species remain uncharacterized. This study aimed to clarify the functions of BbHDA6 (a histone deacetylase gene) in B. balsamifera flavonoid biosynthesis and abiotic stress responses. Methods: We cloned the full-length BbHDA6 gene (1350 bp) and systematically analyzed its molecular characteristics and expression patterns. Heterologous functional validation was subsequently conducted in Arabidopsis thaliana and Nicotiana benthamiana . Transgenic Arabidopsis plants overexpressing BbHDA6 were subjected to ABA, osmotic, and salt stress treatments, and the gene’s role in abiotic stress responses was characterized by combining phenotypic analysis with transcriptome sequencing. Meanwhile, the function of BbHDA6 in flavonoid biosynthesis was investigated in transgenic plants. Results: Results showed that BbHDA6 localizes to the nucleus, is predominantly expressed in the upper leaves of B. balsamifera , and responds to abiotic stress. Overexpression of BbHDA6 in transgenic Arabidopsis enhanced plant tolerance to low ABA concentrations but increased sensitivity to high ABA concentrations. In addition, BbHDA6 regulated salt stress responses in a developmental stage-dependent manner and positively improved osmotic stress tolerance. Transcriptome analysis of BbHDA6 -transgenic Arabidopsis revealed that BbHDA6 modulates key abiotic stress-responsive genes and acts as a negative regulator of flavonoid biosynthetic genes. Furthermore, overexpression of BbHDA6 in N. benthamiana reduced the total leaf flavonoid content by 29.72%–37.18%. Discussion: Collectively, this study is the first to identify BbHDA6 as an epigenetic factor regulating abiotic stress resistance and flavonoid biosynthesis in B. balsamifera , providing a key molecular target for the genetic improvement of plant flavonoid content and stress-resistant traits.

C ₁₈ H ₂₄ N ₂ O ₂ S, monoclinic, P 2 ₁ / c (no. 14), a = 27.3975(7) Å, b = 6.16564(14) Å, c = 9.9182(2) Å, β = 99.202(2)°, V = 1653.86(7) Å ³ , Z =  4, R _gt ( F ) = 0.0586, wR _ref ( F ² ) = 0.1544, T = 100(1) K.