Fossil leaves assigned to the genus Ginkgo are increasingly being used to reconstruct Mesozoic and Tertiary environments based on their stomatal and carbon isotopic characteristics. We sought to provide a more secure basis for understanding variations seen in the plant fossil record by determining the natural variability of these properties of sun and shade leaf morphotypes of Ginkgo biloba trees under the present atmospheric CO2 concentration and a range of contemporary climates in three Chinese locations (Lanzhou, Beijing, and Nanjing). Climate had no major effects on leaf stomatal index (proportion of leaf surface cells that are stomata) but did result in more variable stomatal densities. The effects of climate and leaf morphotype on stomatal index were rather conserved (<1%) and much less than the response of trees to recent CO2 increases. Leaf carbon isotope discrimination (delta) was highest for trees in Nanjing, which experience a warm, moist climate, whereas trees in the most arid site (Lanzhou) had the lowest delta values. Interestingly, the variation in delta shown by leaf populations of trees from China and the United Kingdom was very similar to that of fossil Ginkgo cuticles dating to the Mesozoic and Tertiary, which suggests to us that the physiology of leaf carbon uptake and regulation of water loss in Ginkgo has remained highly conserved despite the potential for evolutionary change over millions of years.