Abstract: Objective: The strain BJQ0011 isolated from Jiuqu can catalyze ester synthesis under aqueous phase. The work aimed to investigate its mechanism for fatty acid ethyl ester synthesis under aqueous phase. Methods: The whole genome of BJQ0011 was sequenced, and bioinformatic analysis was performed to locate the potential ester synthase. Thereafter, gene cloning and expression were applied to identify the ester synthase under aqueous phase. Molecular docking was used to analyze the molecular mechanism of the enzyme that catalyzed the synthesis of fatty acid ethyl esters. Results: BJQ0011 was identified as Burkholderia anthina, and the enzyme encoded by the gene JFN94_RS18195 could catalyze the synthesis of ethyl butyrate, ethyl valerate, ethyl hexanoate, ethyl octanoate and ethyl decanoate under aqueous phase, with the highest efficiency in the synthesis of ethyl octanoate from octanoic acid. The potential catalytic triad of the enzyme was Ser111-Asp241-His274, and Ala22 and Met112 might be involved in the formation of oxygen anion holes. Combined with the results of molecular docking with multiple ligands, the molecular catalytic mechanism for synthesizing fatty acid ethyl esters by the enzyme JFN94_RS18195 was proposed. Conclusion: These results provided the microbiological and enzymatic basis for the synthesis of important flavor fatty acid ethyl esters in baijiu.