Created and shaped by the Columbia River Basalt (CRB) Group volcanism, the Clarkia Miocene lake in northern Idaho renders an exceptional ancient archive of a terrestrial ecosystem formed during the warming period of the Miocene Climate Optimum (MCO). Among different fossil taxonomic groups, the plant mega-fossil Lagerstätten stands out with its high diversity, extreme abundance, and extraordinary preservation of cellular details, in situ biomolecules, and the fidelity of stable isotope signatures. Along with organic geochemistry data derived from its organic rich sediments, the Clarkia deposit offers an unparalleled window into the Earth’s warm past that can be compared with the near future Earth under a high CO2 concentration that doubles the pre-industrial CO2 level. Discovered more than 50 years ago, the Clarkia flora has been the subject of multi-disciplinary research, from paleobotany to paleoliminology during the early phase, to the recovery of biomolecules and stable isotope signatures in the 1990s, and to the recent paleoclimate focused studies. Representing a warm temperate vegetation, the Clarkia flora has yielded more than 150 recognized species for studies of phytogeography, paleo-physiology, phylogenetic, plant-insect interactions, and fossil taphonomy. A suite of new biological and organic geochemical technologies, ranging from the Polymerase Chain Reactions (PCR) to the compound-specific isotope analysis, was first applied to pre-Quaternary plant fossil material in Clarkia. Recently-improved leaf epidermis preparation technique using Clarkia plant material has enabled precise measurements of stomatal apparatus which are critical parameters for the reconstruction of ancient CO2 by the newly developed leaf-gas exchange models. We recently radiometrically dated the interbedded volcanic ash layers at its type locality, P-33, yielding 15.78 ± 0.039 Ma U-Pb zircon ages. The establishment of annually-resolved Clarkia sediments using micro X-Ray fluorescence, petrographic and spectral analyses constrains the P-33 sequence under a millennium human societal timeframe during the peak of the MCO associated with major carbon-cycle perturbations. CO2 reconstructions using the Franks model (one of the leaf-gas exchange models) yielded median middle Miocene CO2 levels above 500 ppm based upon different Clarkia plant fossils of both angiosperm and gymnosperm species. Interdisciplinary research at Clarkia revealed molecular level diagenetic process controlled by the change of paleolimnological conditions, pointing toward the critical role of different microbial communities in mediating key fossilization processes within a clay mineral-rich environment. We review the scientific achievements made based upon Clarkia plant fossils and associated biomolecules and explore new directions of research that the Clarkia plant fossils can potentially offer. The high quality of fossil preservation with precise determination of geochronology, well-constrained sedimentation rates, and demonstrated multiple proxies of climate signals warrant Clarkia plant fossils as desirable material to paleobotany, paleolimnology, and high-resolution paleoclimate research for years to come.