In mammals, ␣-linked GlcNAc is primarily found in heparan sulfate/heparin and gastric gland mucous cell type mucin. ␣-N-Acetylglucosaminidases (␣GNases) belonging to glycoside hydrolase family 89 are widely distributed from bacteria to higher eukaryotes. Human lysosomal ␣GNase is well known to degrade heparin and heparan sulfate. Here, we reveal the substrate specificity of ␣GNase (AgnC) from Clostridium perfringens strain 13, a bacterial homolog of human ␣GNase, by chemically synthesizing a series of disaccharide substrates containing ␣-linked GlcNAc. AgnC was found to release GlcNAc from GlcNAc␣1,4Gal1pMP and GlcNAc␣1pNP substrates (where pMP and pNP represent p-methoxyphenyl and p-nitrophenyl, respectively). AgnC also released GlcNAc from porcine gastric mucin and cell surface mucin. Because AgnC showed no activity against any of the GlcNAc␣1,2Gal1pMP, GlcNAc␣1,3Gal1pMP, GlcNAc␣1,6Gal1pMP, and GlcNAc␣1,4GlcA1pMP substrates, this enzyme may represent a specific glycosidase required for degrading ␣-GlcNAccapped O-glycans of the class III mucin secreted from the stomach and duodenum. Deletion of the C-terminal region containing several carbohydrate-binding module 32 (CBM32) domains significantly reduced the activity for porcine gastric mucin; however, activity against GlcNAc␣1,4Gal1pMP was markedly enhanced. Dot blot and ELISA analyses revealed that the deletion construct containing the C-terminal CBM-C2 to CBM-C6 domains binds strongly to porcine gastric mucin. Consequently, tandem CBM32 domains located near the C terminus of AgnC should function by increasing the affinity for branched or clustered ␣-GlcNAc-containing glycans. The agnC gene-disrupted strain showed significantly reduced growth on the class III mucin-containing medium compared with the wild type strain, suggesting that AgnC might have an important role in dominant growth in intestines.