Description: Diepkloof Rock Shelter (DRS) represents a site of major interest for reconstructing early human behaviours during the Middle Stone Age (MSA). Rock shelters such as DRS also potentially preserve information concerning the environmental context for such behaviours. In this respect the organic matter composition of rock shelter sediments has rarely been investigated in detail, particularly at the molecular level. Here, we used pyrolysis-gas chromatography/mass spectrometry (py-GC/MS) to systematically assess the organic matter composition of bulk sediments within the MSA and Later Stone Age (LSA) sequence at DRS. From this we sought to gain insights into site usage, taphonomy and burning practices. Additionally, we analysed the chain length distribution of leaf-wax n-alkanes as well as their hydrogen and carbon isotopic compositions (dDwax and d13Cwax) to investigate their potential as hydroclimate and vegetation indicators. This constitutes the first leaf-wax isotopic data in a terrestrial context of this antiquity in South Africa. Py-GC/MS shows a dichotomy between stratigraphic units (SUs) of high organic matter content, producing a range of pyrolysis products, including homologous series of long chain n-alkene/n-alkane doublets and alkyl-nitriles, and SUs of low organic matter content, dominated by aromatic, heterocyclic N and polycyclic aromatic hydrocarbon (PAH) pyrolysis products; typical molecular burning products. Several SUs of the Intermediate Howiesons Poort interval exhibit the latter composition, consistent with micromorphological evidence. d13Cwax remains stable throughout the MSA, but leaf-wax n-alkane chain length and dDwax increase during the Late Howiesons Poort interval. Comparison with such patterns in modern plants in the region suggests this represents a shift towards the input of more arid-adapted vegetation into the shelter, driven either by aridification at the site locale or a change in selection practices. Our results suggest that these techniques have further potential in southern Africa and globally at sites where organic matter preservation is high.