Microalgae, with cyanobacteria, are the major primary producers in aquatic, predominantly marine, ecosystems, contributing to the biogeochemical cycling of multiple elements despite their small instantaneous biomass. Their evolutionary history revealed by genomic analyses has shown a complex past that produces a polyphyletic group including organisms that have undergone primary, secondary and tertiary chloroplast endosymbiosis with genetic integration and also horizontal gene transfer. All but one genus of photosynthetic eukaryotes arose by endosymbiosis of a gloeomargarita-like β-cyanobacterium in a eukaryote with the retention of some genes in the plastid, the transfer of more genes to the eukaryote nucleus, and the loss of many others, to produce the Archaeplastida. A second, much later, endosymbiosis of an α-cyanobacterium in a euglyphid amoeba yielded Paulinella. The diversification of the Archaeplastida yielded Glaucophyta, Rhodophyta, Chlorophyta and Streptophyta. Secondary endosymbiosis of red algae in eukaryotes led to microalgae of the ‘red line’, that is, photosynthetic Ochrista (= stramenopiles), Haptophyta, Cryptophyta and Alveolata (dinoflagellates and chromerids). Secondary endosymbiosis of chlorophyte algae in eukaryotes yielded microalgae of the Chlorarachniophyta and Euglenophyta. The ‘red line’ of secondary endosymbionts are dominant marine phytoplankton, possibly related to the occurrence of chlorophyll c that has high absorbance of blue light that dominates in deep ocean waters.