The absolute orientation of the flagellar apparatus in green algal motile cells is a feature of considerable value in studies of green algal systematics and phylogeny. The absolute orientation patterns found in those algae for which this feature is known or can be deduced are reviewed. Counterclockwise absolute orientation occurs in all classes except the Chlorophyceae and is considered primitive, while the clockwise absolute orientation present in most members of the Chlorophyceae is the result of progressive clockwise rotation of components during evolution. Extant intermediates documenting this rotation include Hafniomonas vegetative cells, which show counterclockwise absolute orientation, and Chaetopeltis quadriflagellate zoospores, in which the flagellar apparatus is strictly cruciate except for a slight clockwise offset of the microtubular rootlets. The V-shaped arrangement of the basal bodies in the flagellar apparatus, as well as the presence of proximal sheaths and of two layers of scales on the cell body, further identifies the Chaetopeltis zoospore as a primitive cell type within the Chlorophyceae. Trends towards the exsertion of basal bodies from a flagellar pit, either apically or laterally, the elimination of quadriflagellate cells, and, in the Chlorophyceae, an increasing amount of basal body offset, indicate advancement within the classes. Absolute orientation is conserved during flagellar apparatus replication and development. Events after flagellar apparatus division in the algae studied may be subdivided into component assembly, which is universal and preserves phylogenetically-useful features, and component reorientation, which occurs in relatively few green algae and adapts the flagellar apparatus to specialized functions. From these flagellar apparatus orientation studies, a major reevaluation of evolution within the Chlorophyceae is proposed, with weakly-thalloid algae possessing desmoschisis (e.g. Chaetopeltis) considered primitive, and most other types, including the Volvocales, considered more advanced. The evolution of wall formation does not preclude the formation of scales in primitive chlorophycean genera. In addition, one or more previously undescribed major lineages may exist within the green algae, including one, the Pleurastrum lineage, whose members possess dorsiventrally-flattened motile cells, counterclockwise absolute orientation of the flagellar apparatus, and a phycoplast at cytokinesis. The Chlorophyceae, the Ulvophyceae, and the Pleurastrum lineage are considered to have a common ancestor that resembled the modern genus Pyramimonas, while the Charophyceae is thought to be of more ancient derivation. The ancestors for all classes possessed counterclockwise absolute orientation of the flagellar apparatus and diamond-shaped scales.