Oligotrich ciliates are an abundant and important component of planktonic food webs. Classified together, based on morphology and the arrangement of the oral ciliature, they include sensu lato halteriids, strombidiids, strobilidiids, and tintinnids. The oral ciliature of tintinnids and strobilidiids, the subclass Choreotrichia, is composed of a closed circle of external polykinetids with internal polykinetids, leading to the cytostome. Strombidiid and halteriid species, the subclass Oligotrichia, have an open circle of adoral polykinetids and separate ventral polykinetids. Previous molecular phylogenetic analyses of spirotrichs have placed Halteria grandinella among the stichotrichs. Apart from H. grandinella, only one other small subunit ribosomal RNA (SSrRNA) gene sequence of an oligotrich ciliate (Strombidium purpureum) has been published. Fourteen additional species representative of the major oligotrich orders were collected to determine their phylogenetic relationships. These SSrRNA gene sequences include two strombidiids (Strombidium spp.), one strobilidiid (Strobilidium caudatum), and 11 tintinnid species (i.e. Codonellopsis americana, Eutintinnus pectinis, Eutintinnus sp., Favella panamensis, Metacylis angulata, Metacylis sp., Rhabdonella hebe, Tintinnidium mucicola, Tintinnopsis dadayi, Tintinnopsis fimbriata and Tintinnopsis tocatinensis). The subclasses Oligotrichia (excluding Halteria) and Choreotrichia form a monophyletic group and are sister group to the subclass Stichotrichia with high nodal support. The choreotrichs are confirmed as a monophyletic subclass whereas the halteriids do not cluster with the strombidiids, but within the subclass Stichotrichia. Therefore, the family Halteriidae is transferred to the order Sporadotrichida in the subclass Stichotrichia. The strombidiids form a sister clade to the subclass Choreotrichia. Since there are no clear morphological or genetical synapomorphies for these two groups combined, the separate subclasses Choreotrichia and Oligotrichia are retained. The genetic relationships among tintinnid genera do not correspond to relationships based on lorica morphology: species with agglomerated and hyaline loricae do not form separate branches but are interrelated.