Abstract: By integrating live observation, protargol staining, small subunit ribosomal RNA (SSU rRNA) gene sequencing, and phylogenetic analyses, we investigated the morphology and phylogeny of two oxytrichid ciliates newly recorded from the Chishui River basin, namely Paraurostyla weissei (Stein, 1859) Borror, 1972 and Apoaustralocirrus shii (Shi et al., 1997) Omar et al., 2025. This study provides the first morphologically validated SSU rRNA gene sequence for P. weissei. The results revealed that the Chishui River population of P. weissei was generally consistent with previously described European populations in key morphological traits, including live morphology, cortical granules, cirral and dorsal kinety patterns, and the number of macronuclear nodules and micronuclei, and exhibited relatively stable morphological features. Furthermore, molecular phylogenetic analyses supported its taxonomic identification: the SSU rRNA gene sequence of the Chishui River population showed 99.88%—100% similarity to those of European populations, with 0—2 nucleotide differences, and formed a well-supported clade in the phylogenetic tree. The Chishui River population of A. shii closely matched the diagnostic features of the species: (1) two macronuclear nodules; (2) bright yellow cortical granules; (3) five transverse cirri arranged in two groups. Compared with previously reported populations from Heilongjiang, China, India, Jamaica, and South Korea, the Chishui River population displayed certain population-level variation in body size, number of adoral membranelles, number of dorsal kineties, and number of micronuclei. However, the ranges of key diagnostic features overlapped among populations and should be regarded as intraspecific variation. Molecular phylogenetic results also supported the taxonomic identification of this species: the SSU rRNA gene sequence of the Chishui River population showed 99.94%—100% similarity to those of known populations, with 0—1 nucleotide difference, and clustered with them in the phylogenetic tree. The present study reported new distribution records of the two ciliates in the Chishui River basin, supplemented data on morphological variation among geographically distinct populations, and provided a basis for understanding the distribution patterns and biodiversity composition of ciliates in the Chishui River basin.