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Cyanobacteria are the oldest microorganisms performing oxygenic photosynthesis. Despite their morphological diversity, establishing a taxonomy that reflects evolutionary relationships has always been challenging. Molecular data have helped us to understand some aspects of the complex evolution of the cyanobacteria, but many of the published phylogenetic trees still lack the statistical support on internal branches necessary for reliable conclusions. Recent analyses involving whole genome data have provided us with new insights into cyanobacterial evolution, but taxon numbers are still comparatively small. Ultrastructural characters have the potential to complement molecular data and can help to resolve phylogenetic relationships where sequence data alone are not sufficient. Despite all uncertainties involved, several well supported natural groups started to emerge, whereas other long-standing classical cyanobacterial taxa were shown to be nonmonophyletic assemblages. This article summarizes the current knowledge of phylogenetic research in the cyanobacteria, focusing on the main evolutionary lineages at ordinal level and above. [ABSTRACT FROM AUTHOR]