The diversity found among algae is explained by their evolution. Molecular identification methods have helped explain the phylogeny, or evolutionary relationships, of algae and their evolution from single-celled organisms to more complex organisms. Molecular methods involve comparing the ribonucleic acid (RNA) from different algae, specifically a subunit of ribosomal RNA (rRNA) called 188 rRNA. By studying the nucleic acids contained in 18S rRNA, phycologists have learned that different algae evolved independently of each other, yet the modern forms share many characteristics. Algae provide an example of a polyphyletic organism: Their phyla have different origins.

Algal phyla are also referred to as divisions; they are, from most primitive to most recent on the evolution scale, the following: Euglenophyta, Pyrrhophyta, Phaeophyta, Chrysophyta, Rhodophyta, Charophyta, and Chlorophyta. These phyla belong to two different kingdoms. For example, Phaeophyta and Rhodophyta reside in kingdom Plantae, but the other phyla belong to kingdom Protista. In addition to rRNA, cell structure and pigments can be used to group algae, yet sometimes these groupings appear to hold little logic. For instance, diatoms belong with the Chrysophyta even though diatom rRNA suggests these microorganisms evolved with members of Phaeophyta. The Cyanophyta had been called blue-green algae for many years, but these organisms actually belong with aerobic photosynthetic bacteria.