A C-type lectin (BRA-2) isolated from the acorn barnacle Megabalanus rosa, which was a glycoprotein having an N-linked sugar chain, was deglycosylated by N-glycopeptidase F. The structure of the released sugar chains was determined by a 2-D mapping method after derivatization with a fluorescent reagent, 2-aminopyridine, to be Manα1–6(Manα1–3)Manβ1–4GlcNAcβ1–4(Fucα1–6)GlcNAc and Manα1–6(GlcNAcβ1–2Manα1–3)Manβ1–4GlcNAcβ1–4(Fucα1–6))GlcNAc. The structures were confirmed by matrix-assisted laser desorption ionization mass spectrometry and a comparison with authentic sugar chains by high-pressure liquid chromatography. Various properties of BRA-2 were examined before and after deglycosylation. The susceptibility of BRA-2 to protease digestion was increased by deglycosylation. However, the inhibitory activity toward calcium carbonate crystallization as well as the hemagglutinating activity of deglycosylated BRA-2 was significantly decreased. These results suggest that the sugar chains of BRA-2 are important to both its structural stability and its function.