This research integrates a large morphological data set into a molecular context. Nineteen pellicle characters and 62 states from 13 euglenid taxa were analyzed cladistically. The pellicle morphology of Euglena tripteris (Klebs), Lepocinclis ovata (Conrad), Phacus brachykentron (Pochmann), P. oscillans (Klebs), P. pyrum (Stein), and P. triqueter (Dujardin) is described comprehensively. These data are compared with new information on the pellicle morphology of Euglena acus (Ehrenberg), E. stellata (Mainx), and Peranema trichophorum (Stein) in addition to published data on Entosiphon sulcatum (Dujardin), Euglena gracilis (Klebs), Distigma proteus (Pringsheim), and Petalomonas cantuscygni (Cann and Pennick). Nuclear small subunit (SSU) rDNA sequences provided an independent test for establishing a robust organismal pedigree of the same taxa. A synthetic tree derived from the combined phylogenetic analyses of pellicle morphology and SSU rDNA enabled us to parsimoniously map morphological character states. This approach demonstrated the utility of pellicle morphology for inferring phylogenetic relationships of euglenids and establishing apomorphy-based clade definitions. Three robust clades with unambiguous pellicle-based apomorphies can be recognized within taxa traditionally classified as Phacus: (1) L. ovata and P. pyrum, (2) E. tripteris and P. triqueter, and (3) P. brachykentron and P. oscillans. Taxonomic concerns that emerged from these results are discussed.