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Magnetic prospecting is a rapid, economic and noninvasive method for studying buried near-surface structures of archaeological sites. A new generation of magnetic equipment for field data acquisition and advanced methodology for their data analysis allows to reveal a broad range of buried archaeological targets: walls, columns, foundations, caves, tunnels, tombs, water pipes, kilns, furnaces, ovens, and other objects. However, magnetic survey at archaeological sites is commonly affected by a number of natural and artificial “noise” factors. Such complex conditions require an optimization of current methodology of magnetic survey. The implication of magnetic prospecting for the study of archaeological sites is based on the difference (magnetic contrast) in magnetic properties of archaeological targets and surrounding medium. Two archaeomagnetic provinces were defined according to the magnetic characteristics of archaeological elements, background soils and rocks, and pattern of magnetic anomalies. This allowed us to develop an optimized methodology for high-resolution and reliable archaeomagnetic prospecting in each archaeomagnetic province.