The chromalveolate "supergroup" is of key interest in contemporary phycology, as it contains the overwhelming majority of extant algal species, including several phyla of key importance to oceanic net primary productivity such as diatoms, kelps, and dinoflagellates. There is also intense current interest in the exploitation of these algae for industrial purposes, such as biodiesel production. However, the evolution of the constituent species, and in particular the origin and radiation of the chloroplast genomes, remains poorly understood. In this review, we discuss current theories of the origins of the extant red alga-derived chloroplast lineages in the chromalveolates and the potential ramifications of the recent discovery of large numbers of green algal genes in chromalveolate genomes. We consider that the best explanation for this is that chromalveolates historically possessed a cryptic green algal endosymbiont that was subsequently replaced by a red algal chloroplast. We consider how changing selective pressures acting on ancient chromalveolate lineages may have selectively favored the serial endosymbioses of green and red algae and whether a complex endosymbiotic history facilitated the rise of chromalveolates to their current position of ecological prominence.Algae are emerging as being of key interest in contemporary biological research. As the principal primary producers in oceanic and freshwater communities, algae support the development of complex food webs and biodiverse communities and are responsible for the net flux of nearly 2 gigatons of carbon per year from the atmosphere to the lithosphere, an amount equivalent to or higher than that of tropical rainforests (24,68,122). Understanding why specific algal lineages are more ecologically prominent than others may provide valuable insight into the stability of these ecosystems, particularly as some of the most important taxa are believed to be sensitive to changes in atmospheric and oceanic climates (42, 49), so that phytoplankton community composition is predicted to change considerably in response to current and future climate (28,31,44). In addition, algae are morphologically and physiologically diverse, ranging from microscopic single-celled diatoms and prasinophytes smaller than some bacteria to forests of giant kelps, and differing in their photosynthetic pigments, hence red, green, and brown algae, among others (Fig. 1). The enormous array of biological and biochemical characteristics presented by algae offers great opportunities for exploitation across a wide range of technologies, for example, in the production of biodiesel, industrial chemicals, and even nanotechnologies such as microchips (58,71). This variety offers challenges too, and a much better understanding of the biochemical properties of different algal groups and their chloroplast lineages, which are intimately related to their evolutionary histories, will be required to aid in the identification and culturing of candidate species.In this review, we explore the evolutionary hist...