Background: Tea plants (Camellia sinensis) are widely cultivated cash crops. However, fungal diseases lead to significant reductions in both the yield and quality of tea. Therefore, searching for economical, eco-friendly, and efficient biological control measures is crucial for protecting tea plants from pathogenic fungi. Methods: The confrontation assays were performed to identify the antagonistic bacteria against tea pathogenic fungi and evaluate the antifungal activity of these bacteria. Results: Here, three tea pathogenic fungi were identified: Colletotrichum siamense HT-1, Diaporthe phaseolorum HT-3, and Fusarium fujikuroi HT-4. Notably, D. phaseolorum was the first to be reported in tea plants in China. Some tea pathogenic fungi showed a high relative abundance, suggesting a potential disease risk in tea plantations. Strain GS2Y, isolated from tea rhizosphere soil, exhibited strong antifungal activity against tea pathogenic fungi and represented a novel species within the genus Burkholderia, designated as Burkholderia theae. GS2Y could directly inhibit tea pathogenic fungi by disrupting the cellular structures and protect tea plants from fungal diseases caused by C. siamense HT-1 and D. phaseolorum HT-3. Conclusions: B. theae GS2Y might function as a potentially valuable resource for biocontrol agents, laying the foundation for the development of strategies to manage fungal diseases in tea plants.