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In the present work is described a new on-line solid-phase extraction system using a novel ion imprinted polymer as adsorbent for the preconcentration and determination of mercury(II) in natural water samples by Cold Vapor Atomic Fluorescence Spectrometry (CV AFS). The ion imprinted polymer was prepared by the improved bulk polymerization technique, occurring in only 3 h, based on mercury(II)-dithizone chelate, using methacrylic acid as monomer, ethylene glycol dimethacrylate as cross-linking reagent, 2,2′‑azobisisobutyronitrile as radical initiator, and dimethyl sulfoxide and acetonitrile as porogen solvents. The obtained polymer was characterized by Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), Thermogravimetry (TG), Derivative Thermogravimetry (DTG) and X-ray Diffraction (XRD). The on-line system was mounted by the easy coupling the mini-column packed with the Hg2+-IIP sorbent to the cold vapor system of the spectrometer. The optimum experimental conditions for the on-line preconcentration system were established employing multivariate methodology (two-level full factorial design and Doehlert matrix). Under the optimized conditions, limits of detection and quantification of 0.02 and 0.06 μg L−1, and preconcentration factor of 29 were obtained for the determination of mercury using the developed on-line system, considering a sample volume of 50 mL. Precision expressed as a relative standard deviation (RSD%) was of 5.2% (n = 7) for a standard solution with mercury(II) concentration of 0.5 μg L−1. Then, the on-line system was applied for the selective preconcentration and determination of mercury (II) in four natural water samples, and addition/recovery tests were performed to evaluate the accuracy of the method. All analyzed samples presented Hg2+ concentrations below the limit of quantification of the proposed method and the recovery values found were in range from 90 to 105%.