Aminoglycoside antibiotics exhibit broad-spectrum antibacterial activity, good efficacy, and stability. However, due to the emergence of antibiotic resistance, their use as broad-spectrum antibiotics is restricted. Bacteria producing the bifunctional enzyme, 6′-aminoglycoside acetyltransferase 2″-aminoglycoside phosphotransferase [AAC(6′)-APH(2″)], can modify aminoglycoside antibiotics, leading to the emergence of clinical drug resistance. A method based on ultra-high performance liquid chromatography–mass spectrometry (UHPLC-MS) is reported to monitor the modification of aminoglycoside antibiotics and to screen potential inhibitors of AAC(6′)-APH(2″) from marine natural products. Instead of using purified AAC(6′)-APH(2″), Escherichia coli cells harboring AAC(6′)-APH(2″) were employed. In vivo enzyme assays, conducted in the physiological environment, compensated for the disparity between in vitro responses and those in living cells. The inhibition zone method was used to verify the reliability of the UHPLC-MS results. From a library of 63 marine natural products, Mer-C-3 and Mer-c-8e pyridine alkaloids were shown to provide inhibitory activity against AAC(6′)-APH(2″) in living bacteria. The UHPLC-MS-based approach offers improved speed, convenience, and sensitivity compared with the traditional inhibition zone assay for the screening of enzyme inhibitors. [ABSTRACT FROM AUTHOR]