We outline the results of mineralogical and geochemical analyses of Middle Pleistocene sediments of layer 21 in the Main Chamber of Denisova Cave, Altai. The aim of the study was to reveal a set of mineralogical and trace element markers of the black-colored horizons or lenses and to distinguish them from other types of cave sediments. Results were matched with those relating to a similar set of markers of black-colored horizons in the Holocene part of the section in the East Chamber. Results indicate probable sources of organic and organogenic substances in layer 21. The preservation of geochemical marks was assessed for Pleistocene in comparison with Holocene strata, where those markers are distinct. Black-colored lenses in layer 21 resemble biogenic sediments from Holocene section of the East Chamber. Both layers are characterized by high contents of N-bearing organic matter, P, Zn, Cu, and Cd. In bulk samples from Holocene sediments, numerous fragments of chitin (insect exoskeletons) and patches of newly formed Ca and Ca-Mg phosphates were found. We conclude that these peculiar lenses consist mostly of guano from insectivorous bats, and had undergone deep biodegradation. All black-colored horizons and lenses studied in Denisova Cave have a similar set of geochemical markers and distinctly differ from the adjacent strata by their phase, macro- and trace element compositions.