Stomatal characteristics are used as proxies of paleo-environment. Only a few model species have been used to study the mechanisms of genetic and environmental effects on stomatal initiation. Variation among species has not been quantified. In this paper, results from an in situ reciprocal transplant experiment along an elevation gradient in the northeast Tibetan Plateau are reported, in which the relative effects of genetics (original altitude) and environment (transplant altitude) on stomatal density (SD) and length (SL) were quantified. In Thalictrum alpinum, only the environment significantly influenced SD, with the variance component () of the environment found to be much greater than that of genetics () (). In Kobresia humillis, only genetics significantly influenced SD and SL, with the genetics variance component found to be greater than that of the environment (, for SD). These results suggest that the extent to which genetics and the environment determine stomatal initiation and development is species-specific. This needs to be considered when studying genetic or environmental controls of stomatal initiation, as well as when SD and SL are used as proxies for ancient climate factors (e.g., CO2 concentration).