Ginkgo biloba, a famous living fossil, is the sole survivor of the genus Ginkgo. To make inferences about the glacial refugia that harbored G. biloba, we examined the genetic structure of eight potential refugial populations and plantations using chloroplast DNA (cpDNA) with eight size variants in the trnK1-trnK2 fragment. The data consist of haplotypes from 158 trees collected from eight localities. The majority of the cpDNA haplotypes are restricted to minor portions of the geographical range. Our results suggest that refugia of G. biloba were located in southwestern China. This area is a current biodiversity hotspot of global importance, and may have been protected from the extremes of climatic fluctuations during the Pleistocene. The Ginkgos on West Tianmu Mountain, which were previously considered to be wild by many researchers, may, instead, have been introduced by Buddhist monks.