The Parabotia loaches are an endemic group occured freshwater bodies in the east China. At present six species of this genus have been known in China. Phylogenetic relationships within Parabotia fishes were elucidated based on 35 variable osteological and external morphological characters, which are of phylogenetic significance, in this paper. A total of 440 specimens were examined. Botia pulchra and Botia robusta were designated as an out-group. Skeletal specimens were prepared by the method of Dingerkus and Uhler (1977). Based on the 35 characters, two parsimoniously equal tree were reached for Parabotia fishes (TL = 52 CI 0.84 RI = 0.86), P. lijiangensis + ( P. bimaculata + ( P. fasciata + ( P. banarescui + P. maeulosca))) or P. lijiangensis + ( P. bimaculata + (P. banarescui + (P. maculosa + P. fasciata))). The monophyleticity of Parabotia was decided by possessing fontenelle, an irregular lateral view of metapterygoid, an rectangular lateral view of kinethmoid, three pairs of pharngobranchial, much curved coracoid, nicked upper rostral cap, and absent of sublingual cartilage and the mandibular processes.