The marine ciliate Nothoholosticha is characterized by having a Holosticha-like ciliature pattern but without migratory frontoterminal cirri. However, its systematic position and its relationship to other members of the Holosticha-complex have not yet been resolved. In order to gain deeper insights into these relationships, the small subunit rRNA (SSrRNA) gene and the rRNA internal transcribed spacer and 5.8SrRNA (ITS1-5.8S-ITS2) region of two marine Anteholosticha species, as well as the ITS1-5.8S-ITS2 region of N. fasciola, were sequenced, and molecular trees (BI, ML, NJ and MP trees) were constructed. Although our analyses failed to conclusively resolve the phylogeny of this assemblage, certain conclusions could be drawn. Firstly, Nothoholosticha is a valid genus that is more closely related to Pseudokeronopsis than to other Holosticha-complex genera. Secondly, sequence analyses and phylogenetic trees of several Anteholosticha species revealed a high molecular diversity, which does not support the monophyly of this genus. Thirdly, the current assignment of certain well-known genera, e.g.