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The aim of the article is reconstruction of purpose of ancient settlements construction using a combination of chemical and microbiological indicators. The study object is the Bagai-1 settlement of the Late Bronze Age in the northwestern part of the Crimean Peninsula. The chemical and microbiological properties of the occupation layer within the buildings of various shapes and sizes in different parts of the site have been studied. It was established that the Bagai-1 settlement is a stationary settlement of pastoralists, or was intended for living in the winter. Traces of cattle manure were found everywhere, which is confirmed by the high values of such soil indicators of livestock keeping as urease activity, the number of keratinolytic fungi and thermophilic bacteria in the cultural layer. The results of the research showed that most of the buildings in the settlement were related to livestock keeping. We cannot exclude the joint stay in the premises of both animals and humans, especially in the cold season when livestock was used as a source of heat. However, according to the complex of natural scientific data, no buildings have been identified that could be called exclusively residential, and in all cases the traces oflivestock are much more pronounced than the traces of human habitation. At the same time, vast areas without traces of stone buildings were found at the settlement, but with a high content of mineral forms of phosphates in the cultural layer and high values of magnetic susceptibility, which indicates the entry into the soil of a large amount of ceramics, ash, and pyrogenic residues. The combination of these properties can be considered as an indicator of human habitation.