The rock shelter Mafusing 1 was excavated in 2011 as part of the Matatiele Archaeology and Rock Art or MARA research programme initiated in the same year. This programme endeavours to redress the much-neglected history of this region of South Africa, which until 1994 formed part of the wider ‘Transkei’ apartheid homeland. Derricourt’s 1977 Prehistoric Man in the Ciskei and Transkei constituted the last archaeological survey in this area. However, the coverage for the Matatiele region was limited, and relied largely on van Riet Lowe’s site list of the 1930s. Thus far, the MARA programme has documented more than 200 rock art sites in systematic survey and has excavated two shelters – Mafusing 1 (MAF 1) and Gladstone 1 (forthcoming). Here we present analyses of the excavated material from the MAF 1 site, which illustrates the archaeological component of the wider historical and heritage-related programme focus. Our main findings at MAF 1 to date include a continuous, well stratified cultural sequence dating from the middle Holocene up to 2400 cal. BP. Ages obtained from these deposits are suggestive of hunter-gatherer occupation pulses at MAF 1, with possible abandonment of the site over the course of two millennia in the middle Holocene. After a major roof collapse altered the morphology of the shelter, there was a significant change in the character of occupation at MAF 1, reflected in both the artefact assemblage composition and the construction of a rectilinear structure within the shelter sometime after 2400 cal. BP. The presence of a lithic artefact assemblage from this latter phase of occupation at MAF 1 confirms the continued use of the site by hunter-gatherers, while the presence of pottery and in particular the construction of a putative rectilinear dwelling and associated animal enclosure points to occupation of the shelter by agropastoralists. Rock art evidence shows distinct phases, the latter of which may point to religious practices involving rain-serpents and rainmaking possibly performed, in part, for an African farmer audience. This brings into focus a central aim of the MARA programme: to research the archaeology of contact between hunter-gatherer and agropastoralist groups.