The Glaucophyta include those algae that have endosymbiotic cyanobacteria in the cytoplasm instead of chloroplasts. Because of the nature of their symbiotic association, they are thought to represent unsuccessful intermediates in the evolution of the chloroplast.

The pigments of the Glaucophyta are similar to those of the Cyanophyceae: both chlorophyll a and the phycobiliproteins are present; however, two of the cyanobacterial carotenoids, myxoxanthophyll and echinenone, are absent (Chapman, 1966).

Although similar to cyanobacteria, the cyanelles should be regarded as organelles rather than endosymbiotic cyanobacteria (Helmchen et al., 1995; McFadden, 2001). Cyanobacteria have over 3000 genes whereas cyanelles have about the same number of genes as plastids (about 200 genes). It is clear the cyanelle (and plastid) genomes have undergone substantial reduction during endosymbiosis. Many of the missing genes eventually relocated to the nucleus, while other genes were lost – made redundant in the cyanelles’ new role as an endosymbiont. For example, cyanobacteria have a respiratory electron-chain whereas plastids do not, the respiratory electronchain is coded by the nucleus in eukaryotic algae.

The organisms in the Glaucophyta are very old; McFadden (2001) calls them the coelocanths of endosymbiosis. The Glaucophyta probably branched off the evolutionary tree before the divergence of red and green algae from one another (Keeling, 2004).

The fact that in such syncyanoses one is dealing with composite organisms that exhibit features altogether new and no longer characteristic of either partner alone, led Skuja in 1954 to establish the phylum Glaucophyta. It must be appreciated that the organisms in the phylum represent a very old group, and that, when evolving, they were very plastic and undergoing a great deal of change in the attempt to reach the relatively stable level of a cell with a chloroplast. Such a dynamic group was formed consisting of a large number of organisms not well suited to compete with their more highly developed progeny. Such a situation led to the demise of many of the original members of the Glaucophyta, resulting in the existence today of few extant members of the group.