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Evolutionary relationships of bacteria were traditionally discussed through the dichotomous system of Gram-negative and Gram-positive divisions. It has generally been accepted that each division shares a common evolutionary history and can be recognised by sharing unique features which were not present in distant ancestry based on their Gram reaction. This shared characteristic, termed ‘synapomorphy’, infers common ancestry. This is now being challenged through data obtained from phylogenetic analysis of highly conserved molecules or genes such as rRNA. The pivotal role of the Gram stain in the description of taxonomic units over the past 100 years is now under question.