The small subunit rRNA (SSU rRNA) coding regions sequenced from the euglenoids Petalomonas cantuscygni, Peranema trichophorum, and Khawkinea quartana were used to assess the phylogenetic relationships of these genera within the Euglenozoa. Phylogenies derived from distance, parsimony, and maximum likelihood methods infer that the euglenoids and kinetoplastids form sister clades within a monophyletic assemblage. Distances representative of closely related lineages separate the genera within the Kinetoplastida, whereas larger distance values separate genera within the euglenoid assemblage. The results of the morphological and molecular studies suggest that phagotrophy arose early in the euglenozoan lineage with the subsequent acquisition of phototrophy, osmotrophy, and parasitism. Phagotrophic euglenoids with a pellicle composed of longitudinal strips appear to have diverged prior to genera with helically arranged strips. This study suggests that the hypothetical ancestor to the Euglenozoa was a phagotroph with two flagella, both containing paraxonemal rods. Furthermore, its basal bodies contained proximal cartwheels, were connected by a prominent fiber, and were anchored with three asymmetrically arranged flagellar roots.