This is a comment on the article of Burrough et al. (2012) in which they present a palaeoclimatic reconstruction based on phytolith assemblages from sandy shoreline deposits in the Makgadikgadi Basin, Botswana. While this work highlights a potentially important paleoenvironmental archive in a notably data-poor region, there are several fundamental short-comings in the Burrough et al. work in terms of the calibration of their findings with plant distributions and ecology. Not recognising these limitations in their article, the authors apply palaeoenvironmental indices that are regionally inappropriate, and which we argue in turn render their paleoenvironmental interpretations invalid. With no regionally specific reference collection being established, it may be the misidentification of phytolith morphotypes that has created the paradox that is posed by Burrough et al. ; http://www.elsevier.com/locate/jaridenv ; BMC was funded in part by the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/ 2007-2013) grant agreement no. 258657.