Classification of the ciliates within the subclass Scuticociliatia reflect significant variations regarding their morphologies, life styles, and behaviors (Corliss 1979; Foissner 1996; Lynn and Small 2002). Small (1967) established this taxon as an independent lineage of hymenostomes characterized by their mode of stomatogenesis and the possession of the scutica or scuticovestige, which is a group of basal bodies or kinetosomes that typically arise posterior of, or parallel to, the paroral membrane. It is generally accepted that the subclass Scuticociliatia comprises three orders: Philasterida, Pleuronematida, and Thigmotrichida (Lynn and Small 2002). Li et al. (2006) added a fourth order, Loxocephalida, although the taxonomic rank of this group remains in question (Yi and Song, personal communication). Although morphological and morphogenetic attributes are routinely used to identify species and to deduce the relationships among them, the systematic positions of certain taxa remain ambiguous (Morade and Small 1994; Song and Wilbert 2000). In recent years, ribosomal RNA data have provided support for the recognition of the scuticociliates as a distinct, high ranking group within the class Oligohymenophorea (Li et al. 2006; Ragan et al. 1996; Shang et al. 2006). Molecular data derived from random amplified polymorphic DNA-fingerprinting (RAPD), and restriction fragment length polymorphism (RFLP) have also been used to reconstruct the phylogenetic relationships both within the Scuticociliatia and with related taxa (Shang and Song 2002, 2005; Shang et al. 2003; Stoeck et al. 1998). However, comparisons between different studies reveal that there is much confusion over phylogeny and evolution of taxa within the Scuticociliatia.