Geranylgeranyl diphosphate (GGPP) is the precursor for the biosynthesis of gibberellins, carotenoids, chlorophylls, isoprenoid quinones, and geranylgeranylated proteins in plants. There is a small gene family for GGPP synthases encoding five isozymes and one related protein in Arabidopsis, and all homologs have a putative localization signal to translocate into specific subcellular compartments. Using a synthetic green fluorescent protein (sGFP), we studied the subcellular localization of these GGPP synthases. When these fusion proteins were expressed by the cauliflower mosaic virus 35S promoter in Arabidopsis, GGPS1-sGFP and GGPS3-sGFP proteins were translocated into the chloroplast, GGPS2-sGFP and GGPS4-sGFP proteins were localized in the endoplasmic reticulum, and the GGPS6-sGFP protein was localized in the mitochondria. Both GGPS1 and GGPS3 proteins synthesized in vitro were taken up into isolated intact pea chloroplasts and processed to the mature form. RNA-blot and promoter-β-glucuronidase (GUS) analysis showed that these GGPP synthases genes are organ-specifically expressed in Arabidopsis. GGR and GGPS1 were ubiquitously expressed, while GGPS2, GGPS3, and GGPS4 were expressed specifically in the flower, root, and flower, respectively. These results suggest that each GGPP synthase gene is expressed in different tissues during plant development and GGPP is synthesized by the organelles themselves rather than being transported into the organelles. Therefore, we predict there will be specific pathways of GGPP production in each organelle.