[Objectives] In June 2025, 5 specimens of the genus Sinocyclocheilus were collected from the outlet of an underground river in Pairu Village, Zuozhou Town, Jiangzhou District, Chongzuo City, Guangxi Zhuang Autonomous Region, China. Morphological and molecular biological evidence confirmed that the specimens as a new species, named Sinocyclocheilus pairuensis Li, Liang et Li, sp. nov. [Methods] Morphological characteristics of the 5 collected specimens were measured and compared with related species of the genus Sinocyclocheilus. A Bayesian tree was constructed based on mitochondrial Cyt b genes. MEGA12 was used to calculate the genetic distances between the species of the genus Sinocyclocheilus. [Results] The new species can be distinguished from other congeners by the following combination of characteristics (Figs. 1, 2; Tables 1, 2):1) a humpback at the junction of the head and back; 2) large eyes, with a diameter of 17.0% ~ 19.7% of the head length; 3) covered in scales, complete lateral line, with 53 ~ 58 lateral line scales; 4) dorsal fin with 3 unbranched and 7 branched rays, last unbranched ray rigid at its base, with serrations along its posterior edge; 5) pectoral fins relatively long, with 1 unbranched and 14 ~ 15 branched rays, extending backward to reach or exceed the starting point of the pelvic fins; 6) pelvic fins relatively short, with 1 unbranched and 7 ~ 8 branched rays, not extending posteriorly to the anus. The phylogenetic tree showed that the new species was a monophyletic population (Fig. 4). The intraspecific genetic distance of the new species was less than 0.1%, while the interspecific genetic distance ranged from 2.0% to 15.7% (Appendix 1 and Electronic appendix 1). [Conclusion] Morphological features and phylogenetic analysis supported that the new species belonged to the S. cyphotergous species group of the genus Sinocyclocheilus. It is the first recorded instance of the genus Sinocyclocheilus in the Zuojiang River of the Pearl River Basin. This provides new information into the phylogeny and biogeography of this genus.