In yeast Saccharomyces cerevisiae the N-linked sugar chain is modified at different positions by the addition of mannosylphosphate. The mnn6 mutant is deficient in the mannosylphosphate transferase activity toward mannotetraose (Karson, E. M., and Ballou, C. E. (1978) J. Biol. Chem. 253, 6484-6492). We have cloned the MNN6 gene by complementation. It has encoded a 446-amino acid polypeptide with the characteristics of type II membrane protein. The deduced Mnn6p showed a significant similarity to Kre2p/Mnt1p, a Golgi alpha-1, 2-mannosyltransferase involved in O-glycosylation. The null mutant of MNN6 showed a normal cell growth, less binding to Alcian blue, hypersensitivity to Calcoflour White and hygromycin B, and diminished mannosylphosphate transferase activity toward the endoplasmic reticulum core oligosaccharide acceptors (Man8GlcNAc2-PA and Man5GlcNAc2-PA) in vitro, suggesting the involvement of the MNN6 gene in the endoplasmic reticulum core oligosaccharide phosphorylation. However, no differences were observed in N-linked mannoprotein oligosaccharides between Deltaoch1 Deltamnn1 cells and Deltaoch1Deltamnn1Deltamnn6 cells, indicating the existence of redundant genes required for the core oligosaccharide phosphorylation. Based on a dramatic decrease in polymannose outer chain phosphorylation by MNN6 gene disruption and a determination of the mannosylphosphorylation site in the acceptor, it is postulated that the MNN6 gene may be a structural gene encoding a mannosylphosphate transferase, which recognizes any oligosaccharides with at least one alpha-1,2-linked mannobiose unit.