Abstract: Isoprenoids, namely terpenoids, are the largest and the most structurally varied groups of natural products, which contain more than 30,000 known compounds. All the isoprenoids are biosynthesized from only two C5 precursors in plants, isopentenyl diphosphate and its isomer, dimethylallyl diphosphate. Two distinct pathways of isopentenyl diphosphate biosynthesis exist in plants: the classical mevalonate pathway and the recently unveiled deoxyxylulose 5-phosphate pathway. In this study, we summarize the recent progress on the molecular genetics of the two pathways, specializing in pathways, genes, enzymes, intermediates, subcellular compartments of isoprenoid biosynthesis, crosstalk of the two pathways and metabolic regulation and engineering.