Pepper ( Capsicum annuum) fruits are a rich source of carotenoids. Geranylgeranyl diphosphate (GGPP) is the precursor for carotenoid biosynthesis， and is produced by GGPP synthase (GGPPS)， which belongs to the prenyl transferase (PTS) family. In this study， we identified from pepper genome a total of 8 PTS homologs. Our subcellular localization， enzymatic activity， and expression level analyses proved that， among these homologs， Capana04g000412 is the only functional GGPPS (CaGGPPS1) for carotenoid biosynthesis in pepper fruits. We demonstrated that CaGGPPS1 interacts with a catalytically inactive small subunit homolog protein CaSSUII， and such an interaction promotes CaGGPPS1 enzymatic activity. We also revealed a protein-protein interaction between CaSSUII and a putative phytoene synthase， and a repression of carotenoid accumulation by silencing CaSSUII in pepper fruits. Taken together， our results suggest an essential contribution of the CaGGPPS1/CaSSUII interaction to carotenoid biosynthesis in ripening pepper fruits.