In 2011, citrus crops represented one of the most important fruit productions in the world with more than 131 million tons. Citrus belong to the Rutaceae family able to produce coumarins which constitute a class of secondary metabolites commonly found in higher plants. In these plants, 7-hydroxycoumarin can undergo a subsequent two step enzymatic modification corresponding firstly to the prenylation at C6 and secondly to the closure of a furan ring, leading to furanocoumarins. In parallel to ecological functions in plants, these molecules can be deleterious for humans. They are potential photosensitizers that can cause photophytodermatitis either after skin contact or ingestion followed by UV A exposure. This photosensitization property is a notable problem with Citrus essential oils, such as bergamot oil, since they are extensively used in perfumes. In this study, coumarin and furanocoumarin contents found in 61 citrus varieties are compared and the chemical diversity is discussed with respect to the genetic diversity. Based on hierarchical ascendant classification, coumarins and furanocoumarins can be separated into 4 groups. Each of these 4 groups is logically organized with respect to the already described plant biosynthetic pathways and allows drawing hypotheses on the doubtful biosynthetic origin of compounds. With reference to Citrus diversity obtained from molecular markers, we highlight the genetic crossings which may have resulted in low coumarin and furanocoumarin content varieties. Citrus varieties identified in this study with low coumarin and furanocoumarin content will constitute invaluable genetic resources to breeding programs, promoting citrus species devoid of these toxic molecules.