Our inability to answer many questions regarding the development of metazoan complexity may be due in part to the prevailing idea that most eukaryote “phyla” originated within a short period of geologic time from simple unicellular ancestors. This view, however, is contradicted by evidence that larger groups of eukaryotes share characters, suggesting that these assemblages inherited characters from a common ancestor. Because molecular analyses have had limited success in resolving the relationships of higher eukaryote taxa, we have undertaken a phylogenetic analysis based primarily on morphological characters. The analysis emphasizes characters considered to have a high probability of having evolved only once. Transitions between taxa are evaluated for the likelihood of character-state transformations. The analysis indicates that the evolutionary history of the clade containing the Metazoa has been complex, encompassing the gain and loss of a secondary and perhaps a primary photosynthetic endosymbiont with accompanying changes in trophic level. The history also appears to have included a hetero-autotrophic ancestor that possessed a “conoid” feeding apparatus and may have involved a transformation from a flagellate to an amoeboid body form, a trend toward increased intracellular compartmentation, and the development of complex social behavior. Such changes could have been critical for establishing the underlying complexity required for a rapid diversification of cell and tissue types in the early stages of metazoan evolution.