Comparison and characterization of polysaccharides from natural and cultured Cordyceps on the basis of their chemical characteristics such as glycosidic linkages were performed for the first time using saccharide mapping. The results showed that polysaccharides from most of the natural and cultured Cordyceps had similar responses to enzymatic digestion. These polysaccharides mainly contained (1→4)-β-D-glucosidic linkages, and (1→4)-α-glucosidic, (1→6)-α-glucosidic, 1,4-β-D-mannosidic, as well as (1→4)-α-D-galactosiduronic linkages also existed in some polysaccharides. Especially, natural and cultured Cordyceps polysaccharides could be discriminated on the basis of high performance liquid chromatography profiles of pectinase hydrolysates, which is helpful to control the quality of polysaccharides from Cordyceps. © 2010 Springer-Verlag.