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Despite their importance to rural livelihoods, the economic and environmental sustainability of contemporary communal pastoral systems of the Kalahari is increasingly being put under scrutiny. Using data collected from a survey of randomly selected pastoral households from two districts of Ghanzi and Kgalagadi South, Botswana, this paper outlines the major constraints affecting contemporary extensive pastoral systems. Because of the prevailing semi-arid climate, recurrent drought outbreaks were cited as a common challenge in both study areas together with lack of fenced grazing areas. Stock theft was also highlighted as a challenge, even though it was more pronounced in Kgalagadi South. In Ghanzi area, the other important challenges included loss of livestock due to predation, while stray animals, stock theft and loss of livestock due to road accidents were equally important. Kgalagadi South pastoral households experienced serious shortage of drinking water for their livestock, followed by inadequate grazing land and limited access to distant markets. The preceding, together with several other less prominent challenges revealed in this study, exert pressure on pastoral livelihoods. There is need, therefore, to address these perceived challenges and strengthen resilience through effective policy reviews to secure rural livelihoods.