To clarify the confusion surrounding species identification and state intraspecific variations, this research studied the morphological taxonomy of five species, Kentrophyllum cf. setigerum Petz et al., 1995; Zosterodasys shumerica Aliev, 1990; Frontonia tchibisovae Burkovsky, 1970; Neourostylopsis orientalis Chen et al., 2013; and Apoholosticha cf. sinica Fan et al., 2014, which were collected from Chongming Island’s marsh wetlands. Kentrophyllum cf. setigerum possesses less somatic kineties than K. setigerum (19–26 right and 18–25 left kineties vs 35–40 right and 30 left kineties). Whether Z. shumerica is identical to Z. transversa Foissner et al., 1994, which was presented in a previous report, was negated. The improved diagnosis for the species is provided. Frontonia tchibisovae was confirmed to have three or four micronuclei, and the number of kinetosome rows in its peniculus 3 varied between China and Russia populations. The new population of N. orientalis bears cortical granules, which differs from the original population that has an arrangement of rows across the dorsal bristles. For A. cf. sinica, there are colorless cortical granules on the ventral side of the new population, whereas in the previously reported populations bright orange, spherical granules were clustered around dorsal cilia. Additionally, we sequenced the small-subunit (SSU) rRNA genes of K. cf. setigerum, N. orientalis, and A. cf. Sinica, and compared the new and reported populations. For the first time, we also provide a species list, including 33 ciliates collected from the wetlands based on living observation and silver staining..