The inverse relationship between concentrations of CO2 in the atmosphere (pCO(2)) and the stomatal index of vascular plant has been widely used to estimate ancient levels of atmospheric CO2. However, some atmospheric concentration of CO2 in the geological past (paleo-CO2) estimates show little congruence because they are derived using different correlative methods, or from different fossil plant species with different calibration approaches. Here we apply three methods, including (1) the empirical method of McElwain (1998), (2) the empirical method of Barclay and Wing (2016) and (3) the mechanistic method of Franks et al., (2014) to a single fossil Ginkgo species (Ginkgoites marginatus) to track and assess their consistency of pCO(2) estimates for the Early Jurassic. By using an inter-comparison of three methods, a high degree of consistency in pCO(2) estimates and trends has been observed in two empirical proxy methods. In addition, the mechanistic method and both the empirical methods also show generally good consistent paleo-CO2 estimates at the bed-level. To test the congruence of paleo-CO2 estimates, we also apply all three methods to one additional Ginkgoalean fossil species (Sphenobaiera huangii). All three methods show species-dependent uncertainty in paleo-CO2 estimates when applied to different Ginkgalean fossil species collected from the same fossiliferous bed. Moreover, considering the potential effect of guard cell size to the mechanistic method, the genome size of fossil and living Ginkgo taxa was analyzed based on the significant positive relationship between genome size and guard cell size. The result demonstrates that a likely occurrence of polyploidy in Sphenobaiera huangii may result in underestimated paleo-CO2 when applying mechanistic method due to an increase in the size of the stomatal complex.