An in situ study of post-Palaeolithic blackish pictographs found in an open air rock-shelter, Los Chaparros site (Albalate del Arzobispo, Teruel province, Spain), was carried out to identify the black pigments used. The composition of the pigments was analyzed by means of non-invasive instrumentation, such as a portable Raman spectrometer (RS) and a hand-held energy dispersive X-ray fluorescence (EDXRF) analyzer. In addition, some black natural deposits with a dendritic pattern, typical of manganese compounds, were also in situ analysed with the aforementioned techniques to explore the possibility that post-Paleolithic people used minerals from the surroundings of the Los Chaparros rock-shelter to elaborate the paintings. The results obtained by the EDXRF analyses of black pigments showed differences in composition between a black Levantine deer, in which manganese was present as the main element, and a deep red Schematic pictograph that included manganese as the secondary element. The results of Principal Component Analysis (PCA) of collected EDXRF spectra showed similarities in the elemental composition between the manganese dendrite formations present in the rock-shelter and the black deer. In order to confirm this, the in situ analytical campaign was completed with some analysis in the laboratory by using micro-RS (μ-RS) and X-ray diffraction (XRD) on mineral samples having black crystallisations. Two specimens were taken, one from the black dendrite present in the same rock-shelter and the other from the Los Mases de Crivillén mining area (which is near to Los Chaparros). These analyses revealed that the characteristic bands of Mn–O and Mn–OH bending and stretching vibrations obtained in situ on the black pictograph were the same as those observed in the Raman spectra of the dendrite mineralization of Los Chaparros obtained in the laboratory by μ-RS.