The morphology and phylogeny of two little-known species, Loxodes kahli Dragesco & Njiné, 1971 and L. rostrum Müller, 1786, isolated from freshwater muddy sediments in China, were investigated based on live features, infraciliature, and small subunit ribosomal DNA (SSU rDNA) sequence data. Loxodes kahli is distinguished from its congeners mainly by the number and arrangement of macronuclei (6–17 in one row) and the number of right somatic ciliary rows (11–26). The Chinese populations of L. kahli also exhibit differences with other populations in terms of the body size and the number of right ciliary rows. The characteristics of L. rostrum are consistent with those of previous studies except for the number of right ciliary rows (9–10). The studied species were redefined based on the new information and previous descriptions. This study also gave a brief morphological summary of the species in the genus Loxodes by an identification key. SSU rDNA sequence-based phylogenetic analyses revealed that both species are grouped with their congeners, supporting the monophyly of the genus Loxodes.