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Nitrate nitrogen is an important nitrogen source for tea plants’ growth and development. LBD transcription factors play important roles in response to the presence of nitrate in plants. The functional study of LBD transcription factors in tea plants remains limited. In this study, the LBD family gene <i>CsLBD39</i> was isolated and characterized from tea plants. Sequence analysis indicated that CsLBD39 contained a highly conserved CX₂CX₆CX₃CX domain. The phylogenetic tree assay showed that CsLBD39 belonged to class II subfamily of the LBD family. <i>CsLBD39</i> was highly expressed in flowers and root; we determined that its expression could be induced by nitrate treatment. The CsLBD39 protein was located in the nucleus and has transcriptional activation activity in yeast. Compared with the wild type, overexpression of <i>CsLBD39</i> gene in <i>Arabidopsis</i> resulted in smaller rosettes, shorter main roots, reduced lateral roots and lower plant weights. The nitrate content and the expression levels of genes related to nitrate transport and regulation were decreased in transgenic <i>Arabidopsis</i> hosting <i>CsLBD39</i> gene. Compared with the wild type, <i>CsLBD39</i> overexpression in transgenic <i>Arabidopsis</i> had smaller cell structure of leaves, shorter diameter of stem cross section, and slender and compact cell of stem longitudinal section. Under KNO₃ treatment, the contents of nitrate, anthocyanins, and chlorophyll in leaves, and the content of nitrate in roots of <i>Arabidopsis</i> overexpressing <i>CsLBD39</i> were reduced, the expression levels of nitrate transport and regulation related genes were decreased. The results revealed that CsLBD39 may be involved in nitrate signal transduction in tea plants as a negative regulator and laid the groundwork for future studies into the mechanism of nitrate response.