A culture collection of clonal, axenic cultures of 35 Arthrospira strains and five strains, which were duplicate subcultures of the original isolates, was established. In addition, eight morphological mutants were isolated from cultures of these strains. All strains are different from those belonging to the genus Spirulina as concluded from TEM and PyMS studies. All Arthrospira strains, duplicates and different morphotypes were screened for variation in morphological, ultrastructural, physiological and biochemical characters for taxonomic purposes. Special emphasis was put on the analysis of factors which influence the morphology of the trichome helix, as this is the feature most characteristic forArthrospira strains. For example, the orientation of coiling was found to be influenced by genetic drift or the growth temperature, but can also be reversed by mechanical impact. Studies were also made on the ability to utilize sugars for growth. None of the strains grew on sucrose, but many grew on glucose and/or fructose. Growth in the presence of sucrose under photoheterotrophic conditions required an adaptation process, though sucrose is not being utilized for growth. Analysis of fatty acid composition of all strains revealed quantitative differences between strains, most markedly in the unsaturated fatty acid fraction. Repeat experiments showed the same results each time, indicating the value of this approach for identification purposes. Similarly, lectin-binding to cell surface structures proved to be a useful approach for differentiation between strains. Analysis of the whole cell composition by pyrolysis mass spectrometry (PyMS) did not confirm the clusters based on other phenotypic characters, but showed that there is a high similarity between duplicate strains or different morphotypes derived from the same stock. Numerical analysis of the data for 28 characters resolved the helical strains in two phenotypic clusters which show a high correlation to the two molecular clusters based on ARDRA of the ITS of the same set of strains. The helical trichome morphology of the strains showed the highest correlation to either of the clusters. Comparison of species descriptions and morphological characters of the strains, as determined in the presented work, indicate, that phenotypic cluster I is composed of Arthrospira maxima, A. fusiformis and A. indica, while A. platensis forms phenotypic cluster II