The present work aims at understanding the composition and source of the red rock art pigments used by hunter-gatherer groups during the late Holocene in southern Patagonia (southernmost South America), by combining micro X-ray fluorescence (μXRF) and Raman spectroscopy. In the first place, μXRF geochemical data do not reveal any significant compositional contrast between anthropogenic pigments and altered basalts but, instead, only different degrees of basalt alteration. Thus, past human populations inhabiting the Pali Aike volcanic field might have locally found the raw material to obtain red pigments from highly weathered basalt outcrops and/or at less than 20 cm depth, where basalt-derived saprolite is widespread. On the other hand, Raman spectroscopy allows distinguishing different hematite populations based on the width and position of the 226 cm−1 band, being the former a proxy of hematite crystallinity. Natural hematite, derived from basalt alteration, shows a relatively low crystallinity and a wide spectrum of Raman parameters, whereas anthropogenic hematite from red rock art pigments shows higher crystallinity and more clustered Raman parameters, indicating possible heating processes of the latter. In addition, the low crystallinity recorded in hematite from an archaeological grindstone suggests that it was used to grind the raw material, a step prior to heating.