The fungal wall contains a small proportion of alkali-extractable water-soluble heteromannans (F1SS). They are the glycidic moiety of glycoproteins that have important roles in the biology of fungi. A considerable number of these polysaccharides has been described, differing in composition or linkage types. Their structure is similar in all species of a well-delimited genus, and teleomorphs and their corresponding anamorphs. Therefore, these polysaccharides have been used as chemotaxonomic markers at the genus level. Here we review cases where they have been found to resolve relationships around the genus level, and assess their phylogenetic informativeness in the delineation of taxa at family and higher ranks in the ascomycetes by comparison with molecular trees. Generally, the correlation is extremely good, from the species to the class level, though there are some divergences. In particular, comparisons suggest that the concept of the Sordariomycetes may eventually require revision as more molecular data become available. An analysis of the different chemical structures of these polysaccharides can lead to the proposal and testing of phylogenetic hypotheses, in a parallel manner to those generated from molecular trees. These molecules serve as an independent character similar to morphological or molecular characters.