Glycan structures are synthesized by a series of reactions conducted by glycosylation‐related (GR) proteins such as glycosyltransferases, glycan‐modifying enzymes, and nucleotide‐sugar transporters. For example, the common core region of glycosaminoglycans (GAGs) is sequentially synthesized by peptide‐O‐xylosyltransferase, β1,4‐galactosyltransferase I, β1,3‐galactosyltransferase II, and β1,3‐glucuronyltransferase. This raises the possibility that functional impairment of GR proteins involved in synthesis of the same glycan might result in the same phenotypic abnormality. To examine this possibility, comprehensive silencing of genes encoding GR and proteoglycan core proteins was conducted in Drosophila. Drosophila GR candidate genes (125) were classified into five functional groups for synthesis of GAGs, N‐linked, O‐linked, Notch‐related, and unknown glycans. Spatiotemporally regulated silencing caused a range of malformed phenotypes that fell into three types: extra veins, thick veins, and depigmentation. The clustered phenotypes reflected the biosynthetic pathways of GAGs, Fringe‐dependent glycan on Notch, and glycans placed at or near nonreducing ends (herein termed terminal domains of glycans). Based on the phenotypic clustering, CG33145 was predicted to be involved in formation of terminal domains. Our further analysis showed that CG33145 exhibited galactosyltransferase activity in synthesis of terminal N‐linked glycans. Phenotypic clustering, therefore, has potential for the functional prediction of novel GR genes.