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Since the basic biochemical mechanisms of photosynthesis are remarkably conserved among plant species, genetic modification approaches have so far been the main route to improve the photosynthetic performance of crops. Yet, phenotypic variation observed in wild species and between varieties of crop species, implies there is standing natural genetic variation for photosynthesis offering a largely unexplored resource to use for breeding crops with improved photosynthesis and higher yields. The reason this has not been explored yet is that the variation probably involves thousands of genes, each contributing only little to photosynthesis, making them hard to identify without the proper phenotyping and genetic tools. This is changing though, and increasingly more studies report on quantitative trait loci (QTLs) for photosynthetic phenotypes. So far, hardly any of these QTLs are used in marker assisted breeding or genomic selection approaches to improve crop photosynthesis and yield, and hardly ever are the underlying causal genes identified. We propose to take the genetics of photosynthesis to a higher level, and identify the genes and alleles nature has used for millions of years to tune photosynthesis to be in line with local environmental conditions. We will need to determine their physiological function, and design novel strategies to use this knowledge to improve crop photosynthesis through conventional plant breeding, based on readily available crop plant germplasm. In this work, we present and discuss the genetic methods needed to reveal natural genetic variation, and elaborate on how to apply this to improve crop photosynthesis.