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To further our understanding of the formation of Denisova Cave sediments, we have employed a microstratigraphic approach to the study of the site stratigraphy, using micromorphology and supplemented by spatially resolved elemental mapping to reconstruct the past depositional and post-depositional environments and clarify the use of the cave by hominins and other animals during the Middle and Late Pleistocene. We examined 24 micromorphological thin sections from several of the stratigraphic units exposed in both the East and Main Chambers in 2014 and 2016, including both occupation horizons and sterile karstic deposits. We observe that the Denisova sediments are predominantly geogenic in composition, with the main mineralic components comprising 1) sand-sized particles of quartz/quartzite, schist, and limestone; 2) silt-sized grains of quartz, mica and calcite, 3) clay, 4) mm- to cm-sized limestone clasts, and grains of metamorphic rocks, and 5) clasts of bedded silt and clay (rip-up clasts). However, we also note that there are significant quantities of biological material included within this sedimentary matrix, such as bone fragments and splinters, occasional charcoal, biogenic silica, and frequently occurring sand- to granule-sized coprolite fragments. The coprolites are present as suites of recurring morpho-types, presumably associated with different animals, in varying states of preservation. We also record physical and chemical modification of the sediments and their inclusions. Post- and syn-depositional chemical modification (diagenesis) is represented by the presence of apatite (dahllite) rims on limestone clasts, localised dissolution of calcite sand, and sesquioxide mobilisation, as well as occasional degradation of bone inclusions. Physical transformations of the sediments include aligned clay particles and micro-faulting that mirror the deformation/slumping features recorded in the field. Infilled animal burrows krotovinas) are evident in the field, and in thin section smaller scale bioturbation by small soil fauna (e.g., isopods, worms)is concentrated in the upper layers. Finally, we identify platy microstructures in the upper layers of both chambers, reflecting periods of cooler temperatures and the concomitant disturbance of sediments through ice lensing and frost heave. These micromorphological results provide additional insights into the depositional history and use of the cave during the period of occupation by Denisovans and Neanderthals.