This chapter explores a range of morphological and ultrastructural characters derived from classical literature of plant morphology and more data from cell biology. As much as possible, characters were selected and coded to allow for comparison across all plant groups used in the analysis. Phylogenetic analyses were carried out based on 132 ultrastructural, biochemical and developmental characters to develop a hypothesis for the principal lineages of extant land plants, in particular the relationships among and within hornworts, liverworts, and mosses. As further developmental and ultrastructural studies are carried out, character state homology should be better defined and lead to more definitive answers with respect to the phylogeny of land plants. The combined data set resulted in 26 most parsimonious (MP) trees in which bryophytes were not monophyletic. Hornworts were the sister group to the remaining land plants, and mosses and liverworts were monophyletic, and formed the sister group to vascular plants.