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The lack of anoxic environments in arid lands makes well-preserved fossil pollen difficult to find. The scarcity of continental palaeobotanical data in tropical arid zones restricts the understanding of aridification processes in these endangered ecosystems. It is essential to improve the knowledge about their environmental histories during the Holocene, and therefore we attempt to investigate the causes and describe the patterns of vegetation change in northern Namibia. With that aim we analyzed pollen from fossil hyrax dung that accumulated over long periods of time by sampling stratigraphically coherent sequences in five radiocarbon-dated middens. The fossil hyrax middens were found in rock shelters on the eastern desert edge in the northwestern Kaokoveld, within the so-called Nama-Karoo biome. This is an ecotonal area between the Namib Desert and the Savanna biomes which reflects features from both systems and its life form composition largely depends on an erratic rainfall pattern. Thirty-three samples were analyzed for pollen and the pollen record reflects a non-continuous vegetation history over the last 5200 yr with a hiatus between ca. 4200 and 1690 yr BP. The pollen spectra reflect arid savanna vegetation with a marked increase in the tree/grass ratio from ca. 1300 cal yr BP. The most likely cause for this change is a decline in moisture that we relate to intrinsic savanna dynamics, with early pastoralism, megahervibore migration and changes in the hyrax diet playing a minor role.