In this thesis studies of the structures of the heterocyst glycolipids of two species of Cyanobacteria, Anabaena cylindrica and Aphanizomenon flos-aquae have been undertaken to provide a better understanding of Cyanobacteria. Early chapters introduce the Cyanobacterium family and the preparation procedures for the heterocyst glycolipids in our studies. These chapters are separated by an introduction of chromatography and mass spectrometry with emphasis on the techniques used in these studies. The remaining chapters discuss the use of GC/EIMS, GC/CIMS, LC/APCIMS and LC/ESMS, MS/MS for the characterisation of the heterocyst glycolipids in the extracts. The GC/MS techniques used with permethylated, deutero-permethylated and trimethylsilylated derivatives of the intact heterocyst glycolipids (obtained from different bands on TLC from Anabaena cylindrica), methoxime glycolipids, aglycones and methoxime aglycones enabled these compounds to be characterised. Complementary structural information was provided by the GC/EI and GC/CI mass spectra of various derivatives. The LC/ESMS and LC/APCIMS studies proved to be effective in both positive and negative ionisation modes. Six glycolipids including two novel ones were detected from two species by these techniques. Band HG-A was shown to contain 1-(O-α-D-glucopyranosyl)-hexacosanediol, 1-(O-α-D-glucopyranosyl)-octacosanetriol and 1-(O-α-D-glucopyranosyl)-octacosanediol, While the keto-compounds, 1-(O-α-D-glucopyranosyl)-keto-hexacosanol, 1-(O-α-D-glucopyranosyl)-keto-octacosanediol and 1-(O-α-D-glucopyranosyl)-keto-octacosanol were found exist in Band HG-B. Besides, the related isomers were also detected. Additionally two heterocyst glycolipids were identified in Band HG-A from Aphanizomenon flos-aquae. A new band on TLC containing heterocyst glycolipids from Aphanizomenon flos-aquae was found and studied by LC/ESMS and LC/APCIMS. Possible structures were proposed.