Peculiar Early Permian palaeontological and sedimentological features are reviewed from South China, including characteristic Early Permian cold-water Gondwanan brachiopod taxa and faunas from Sichuan and Guizhou provinces, widespread rosettes and irregular aggregates of calcite prisms ('Chrysanthemum Stones') within the Qixia limestones, and lack of significant Early Permian reef buildups. The occurrences of these features are at odds with the currently widely held view that South China was located in a palaeotropical, warm-water setting throughout the Permian and hence harboured a highly diverse shallow marine biota. In this paper, I propose a working hypothesis, suggesting that influence of at least cool water masses may have intermittently occurred in South China during the Early Permian, which facilitated the formation of the cool water-influenced palaeontological and sedimentological features and promoted the interchanges of cool to cold water marine faunas between the Gondwanan and Boreal Realms. These cool water masses may have been transported to low-latitude regions as deep currents from northern and eastern shelves of Gondwanaland and upwelled along the western coast of South China as well as within the relatively deep-water basins of central South China. Prevalence of these meridional, north-directed deep cold water currents during the Early Permian may have been related to the glaciation event of Gondwanaland. An alternative and/or additional source of cooling may have also originated from strong easterly palaeoequatorial boundary currents operating within the Palaeotethys at times during the Early Permian, inducing and/or enhancing upwelling of cool to cold water masses in the eastern Palaeotethys. This latter scenario is analogous to the occasional 'La Nina' effect (opposite to the 'El Nino' effect) at the equatorial belt of the modern Pacific Ocean.