The atmosphere and terrestrial ecosystems are fundamentally coupled on a variety of time–scales. On short time–scales, this bi–directional interaction is dominated by the rapid exchange of CO2, water and energy between the atmosphere and the land surface; on long time–scales, the interaction involves changes in ecosystem structure and composition in response to changes in climate that feed back through biophysical and biogeochemical mechanisms to influence climate over decades and centuries. After briefly describing some early pioneering work, I focus this review on recent advances in understanding long–term ecosystem–atmosphere interactions through a discussion of three case studies. I then examine how efforts to assess the stability and resilience of ecosystem–atmosphere interactions over these long time–scales using Dynamic Global Vegetation Models are hampered by the presence of important functional diversity and heterogeneity within plant communities. Recent work illustrates how this issue can be addressed through the use of Structured Ecosystem Models that more accurately scale between the short–term physiological responses of individual plants and the long–term, large–scale dynamics of heterogeneous, functionally diverse ecosystems.