Most species in the anaerobic ciliate family Caenomorphidae Poche, 1913 lack detailed descriptions based on modern morphologic and molecular methods. In this report, two species, Caenomorpha medusula Perty, 1852 and Sulfonecta uniserialis (Levander, 1894) Jankowski, 1978, were isolated from freshwater anaerobic sediments in Qingdao, China. Another population of C. medusula was recorded from Boise, Idaho, USA. We reinvestigated live morphology, ciliature, and the small-subunit (SSU) rRNA gene sequence of both species. The current study supports the opinion of Jankowski that, due to the variation in macronuclear nodule number, this character is of limited taxonomic significance in C. medusula. Scanning electronic micrographs clearly reveal that this species has one posterior spine. The China population of Sulfonecta uniserialis corresponds well with previously described populations in having a single macronucleus, a complex posterior spine, and one bell kinety. Our phylogenetic analyses reveal that the Caenomorphidae is monophyletic. However, the placement of the family is uncertain as it forms a closer relationship with the Litostomatea but with only a medium support value.