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This study utilizes geostatistical modelling of magnetic susceptibility (MS) for geophysical prospection of archaeological stratigraphy at the Middle Stone Age rock shelter site of Pinnacle Point 5-6 North. These models are overlaid onto high-resolution photography of the stratigraphic sequence to study the lateral and vertical changes within the magnetic signature of the archaeological sequence and correlate these changes to micromorphological interpretations previously made at the site. In situ analysis is reinforced by laboratory magnetic mineralogical analysis utilizing MS; frequency-dependent susceptibility (chi(FD)); isothermal remanent magnetization; and anhysteric remanent magnetization to understand the composition of the magnetic minerals creating the in situ signature. This study shows that there is consistent variation in the magnetic signatures of the sequence that can be mapped with in situ MS; there is a correlation with laboratory analysis of magnetic mineralogy, which provides insight into changes in human behaviour; and our models correlate well with micromorphological interpretations of the site. info:eu-repo/semantics/publishedVersion