Conchophthirus curtus is a scuticociliate found in the mantle cavity of unionid bivalve mussels; it is considered by most to be an endocommensal. It was previously redescribed and its morphogenesis has been carefully defined and evaluated. Conchophthirus stomatogenesis along with its enigmatic deep kinetosomal unit as compared with other scuticociliates, peniculines, and peritrichs suggested possible homologies and affinities. Thus, a comparison of Conchophthirus with common molecular markers to all other ciliates was a goal of this study. We collected Conchophthirus spp. in California from two unionid bivalve hosts: Anodonta californiensis in the Pit River and Lake Merced, and Margaritifera falcata from the Trinity River. The ciliates analyzed were predominantly C. curtus although other conchophthirids were present. The small subunit rRNA and the cytochrome c oxidase subunit 1 genes were sequenced. Phylogenetic analyses of these data were analyzed and maximum likelihood for the small submit rRNA dataset and neighbor-joining for the cytochrome c oxidase subunit 1 dataset. The cytochrome c oxidase subunit 1 sequences obtained from M. falcata populations were virtually identical. The analysis placed these sequences with 96% bootstrap support as sister to Dexiotricha sp. The small submit rRNA sequences obtained from populations from both hosts were almost identical, and they showed them to be sister, with 99% support to two unpublished sequences from Chinese populations of Conchophthirus cucumis and C. lamellidens, and sister to a Dexiotricha sp. These data and their analyses confirm Conchophthirus to be a scuticociliate, but not closely related to either philasterine or pleuronematine scuticociliates nor the peniculines or peritrichs. Further analysis awaits additional data. The North American distribution of Conchophthirus, niche analyses, and potential homologous structures are discussed as well as the use of these endocommensals as indicators of water quality and pollution.