A new concept is presented for green analytical applications based on coupling on-line high-intensity focused ultrasound (HIFU) with a sequential injection/flow injection analysis (SIA/FIA) system. The potential of the SIA/HIFU/FIA scheme is demonstrated by taking mercury as a model analyte. Using inorganic mercury, methylmercury, phenylmercury, and diphenylmercury, the usefulness of the proposed methodology for the determination of inorganic and total mercury in waters and urine was demonstrated. The procedure requires low sample volumes and reagents and can be further applied to all chemical reactions involving HIFU. The inherent advantages of SIA, FIA, and HIFU applications in terms of high throughput, automation, low reagent consumption, and green chemistry are accomplished together for the first time in the present work.