Abstract The heterocyte (heterocyst) glycolipid (HG) content of heterocytous (heterocystous) cyanobacteria can principally be separated into two different types. In the first type, the aglycone moiety attached to the sugar headgroup exclusively contains hydroxyl functionalities resulting in the formation of HG diols and HG triols. In the second type, one of the hydroxyl groups is replaced by a ketone functionality giving rise to HG keto-ols and HG keto-diols. In the N2-fixing heterocytous cyanobacterium Microchaete sp. PCC 7126 both types of HGs were dominant and consisted primarily of two structural isomers each of the HG28 diol and HG28 keto-ol. In addition to these well-characterized HGs, Microchaete sp. PCC 7126 also contained a yet undescribed type of HG that based on comparison of retention times, molecular weight and mass spectrometry consisted of a hexose headgroup attached to an aglycone moiety with 28 carbon atoms at which two instead of one ketone functionalities were attached. Hence, the novel HG structure was identified as HG28 diketone. This study thus provides further evidence for the large structural diversity of HGs, which allows chemotaxonomic profiling of heterocytous cyanobacteria and in turn studying the community composition of these important diazotrophs in the geological rock record.