Since molecular phylogenies of stichotrich ciliates started to be published, some remarkable contradictions to morphology-based classifications have been reported, such as the Convergent Evolution of Urostylids and Uroleptids (CEUU) hypothesis, the Halteria paradox, the polyphyly of Oxytricha and of Stichotrichia. We hypothesized the internal phylogeny of 18S-rDNA from 53 morphological species of stichotrichs and their relationships with Hypotrichia and Oligotrichia using parsimony and neighbor-joining methods, including new data from Pseudouroleptus caudatus and Strongylidium pseudocrassum. Competing phylogenetic scenarios were compared using statistical tests, and the results suggest the reconsideration of both CEUU and the position of Halteria among flexible-body oxytrichids. The polyphyly of Oxytricha was not rejected and the monophyly of Stichotrichia was accepted based on parsimony analysis if Pseudoamphisiella is considered an external (discocephalid related) taxon.