Sources, properties and mechanisms of formation of mercury species mainly in aquatic ecosystems are reviewed. Methods of isolation and purification using classical sequential leaching, solvent extraction, microwave extraction and modern techniques, such as supercritical fluid extraction and solid phase extraction, are discussed. Hyphenated techniques combining gas chromatography with spectrometric detectors, and liquid chromatography and capillary electrophoresis with UV-VIS spectrophotometric detectors, atomic absorption, atomic emission and atomic fluorescence detectors or electrochemical detectors are described. Some recommendations for sample collection and treatment and for quantification of individual mercury species are given.