The classification of algae into taxonomic groups is based upon the same rules that are used for the classification of land plants, but the organization of groups of algae above the order level has changed substantially since 1960. Research using electron microscopes has demonstrated differences in features, such as the flagellar apparatus, cell division process, and organelle structure and function, that are important in the classification of algae. Similarities and differences among algal, fungal, and protozoan groups have led scientists to propose major taxonomic changes, and these changes are continuing.

Division-level classification, as with kingdom-level classification, is tenuous for algae. For example, some phycologists place the classes Bacillariophyceae, Phaeophyceae, and Xanthophyceae in the division Chromophyta, whereas others place each class in separate divisions: Bacillariophyta, Phaeophyta, and Xanthophyta. Yet, almost all phycologists agree on the definition of the respective classes Bacillariophyceae, Phaeophyceae, and Xanthophyceae.

The classes are distinguished by the structure of flagellate cells (e.g., scales, angle of flagellar insertion, microtubular roots, and striated roots), the nuclear division process (mitosis), the cytoplasmic division process (cytokinesis), and the cell covering. Many scientists combine the Micromonadophyceae with the Pleurastrophyceae, naming the combined group the Prasinophyceae.  “Phylum” and “division” represent the same level of organization; the former is the zoological term, the latter is the botanical term

Properties of Major Algal Taxonomic Groups