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Past studies in plant phylogenetics have shed light on how the geological history of our planet shaped plant evolution by establishing well-known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). Under this approach, information is transferred from geology to botany, by interpreting data in light of geological processes. In this synthesis, I propose a conceptual shift in this traditional approach to specifically transfer information from botany to geology. This conceptual shift follows the goals of the emerging field of geogenomics and emphasizes that plant phylogenetics can go beyond investigating patterns in light of landscape change, to reduce the inherent uncertainty in models of paleotopography, river system structure, and land connections through time. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data, and what makes some groups of plants excellent model systems for geogenomics research. This synthesis highlights the critical role of classical botanical knowledge in identifying good study systems to unveil long-standing questions on how the earth evolved with the use of plant DNA.