Anp1p, Van1p and Mnn9p constitute a family of membrane proteins required for proper Golgi function in Saccharomyces cerevisiae. We demonstrate that these proteins colocalize within the cis Golgi, and that they are physically associated in two distinct complexes, both of which contain Mnn9p. Furthermore, we identify two new proteins in the Anp1p-Mnn9p-containing complex which have homology to known glycosyltransferases. Both protein complexes have alpha-1, 6-mannosyltransferase activity, forming a series of poly-mannose structures. These reaction products also contain some alpha-1, 2-linked mannose residues. Our data suggest that these two multi-protein complexes are responsible for the synthesis and initial branching of the long alpha-1,6-linked backbone of the hypermannose structure attached to many yeast glycoproteins.