This thesis used molecular phylogenetic techniques to investigate diversity in the conjugating green algae. The conjugating green algae are closely related to land plants and evolution within the group provides a good analogy of how evolution may have proceeded in the lineage that gave rise to land plants. I developed a dataset of the genes coxIII, psaA and rbcL with 109 taxa to determine phylogenetic relationships of the families and genera. I found that the order Zygnematales is not monophyletic and that Spirogyra was the first to branch. The order Desmidiales is monophyletic if one includes the genus Roya. The family Peniaceae is not monophyletic. The genera Cosmarium, Cylindrocystis, Mesotaenium, Penium, Spondylosium, Staurodesmus and in later studies Desmidium and Hyalotheca were found to be paraphyletic or polyphyletic.

Investigation of cell division syndromes among filamentous Desmidiaceae revealed greater diversity than was previously reported. Notable among these discoveries is that Spondylosium pulchrum displays the Desmidium-type cell division, Spondylosium pulchellum the Cosmarium-type, and Spondylosium tetragonum the newly described Teilingia-type cell division. The relationship among the syndromes was inferred from phylogenetic analysis of the species that revealed a single lineage comprising filamentous and colonial species and multiple modes of cell division. This suggests that even the fundamental process of cell division can be highly modified. Results from this study also resulted in the taxonomic resurrection of the genus Didymoprium, as well as the creation of the new genus Isthmocatena and the combinations Didymoprium grevillei, Desmidium pulchrum, and Isthmocatena pulchella.

Investigations of the Gonatozygaceae revealed unexpected diversity in Gonatozygon brebissonii and G. kinahani. Structural measurements were sufficient to distinguish among strains of Gonatozygon species except for Gonatozygon brebissonii. We have probably underestimated genetic and species diversity in this family. In contrast, the structurally distinct species Triploceras gracile, was found to be closely related to Micrasterias. This relationship was confirmed by sequencing and phylogenetic analysis of the nuclear encoded EF1α, EIF4 and TUA. The results of this study indicate that Triploceras is probably actually bilaterally symmetric, although it has been treated as a radially symmetric species.