The giant panda (Ailuropoda melanoleuca) is one of the most endangered animals in the world, and it is recognized worldwide as a symbol for conservation. A previous study showed that wild and captive pandas were exposed to toxins in their diet of bamboo, but the ultimate origin of these toxins is unknown. Here we show that atmospheric deposition is the origin of heavy metals and persistent organic pollutants (POPs) in the diets of captive and wild Qinling giant pandas. Atmospheric deposition averaged 115 and 49 g m-2 yr-2 at China's Shaanxi Wild Animal Research Center (SWARC) and Foping National Nature Reserve (FNNR), respectively. Atmospheric deposition of heavy metals (As, Cd, Cr, Pb, Hg, Co, Cu, Zn, Mn and Ni) and POPs at SWARC was higher than at FNNR. Soil concentrations of the aforementioned heavy metals other than As and Zn also were significantly higher at SWARC than at FNNR. We conclude that efforts to conserve the Qinling subspecies of panda may be compromised by air pollution attendant to China's economic development. Improvement of air quality and reductions of toxic emissions are urgently required to protect China's iconic species.