The presence of stomata is a diagnostic trait of all living and extinct land plants with the exception of liverworts. They are preserved widely in the fossil record from anatomically pristine stomatal complexes on permineralized and charcoalified stems of the earliest land plants dating back >400 million years to isolated guard cell pairs in Quaternary aged palynological samples. Detailed study of fossil stomatal complexes has been used to track the evolution of genome size and to reconstruct atmospheric composition, to circumscribe new species to science and to bring ancient landscapes to life by providing both habitat information and insights on fossil plant ecophysiological function and life-form. This review explores how fossil stomata can be used to advance our understanding of plant, environment and atmospheric evolution over the Phanerozoic. We compare the utility of qualitative (e.g. presence/absence of stomatal crypts) versus quantitative stomatal traits (e.g. amphistomaty ratio) in palaeoecological reconstructions. A case study on Triassic-Jurassic Ginkgoales is provided to highlight the methodological difficulty of teasing apart the effect of genome size, ploidy and environment on guard cell size evolution across mass extinction boundaries. We critique both empirical and mechanistic stomatal-based models for palaeo-CO₂ reconstruction and highlight some key limitations and advantages of both approaches. Finally we question if different stomatal developmental pathways have ecophysiological consequence for leaf gas exchange and ultimately the application of different stomatal-based CO₂ proxy methods. We conclude that most studies currently only capture a fraction of the potential invaluable information that can be gleaned from fossilized stomata and highlight future approaches to their study that better integrate across the disciplinary boundaries of palaeobotany, developmental biology, palaeoecology and plant physiology.