The genus Lepturichthys is endemic in China, including two valid species, L. fimbriata and L. dolichopterus. The former is widely distributed in the Upper and Middle Yangtze River, while the latter only in Minjiang River. In the present study, the mitochondrial cytochrome b gene sequences were analyzed for 20 individuals of L. fimbriata collected from the Upper and Middle Yangtze River and eight individuals of L. dolichopterus collected from Minjiang River. This paper aimed to investigate the geographical speciation process of the genus Lepturichthys. The results showed that the genetic variations among different haplotypes of L. fimbriata ranged from 0.1% to 1.8%, with an average of 0.7%, and from 0.6% to 1.3%, with an average of 0.7% among different haplotypes of L. dolichopterus. The variations between L. fimbriata and L. dolichopterus were also very low, ranging from 0.2% to 1.8%, with an average of 0.9%. Two methods, Neighbor Joining (NJ) and Bayesian analysis (BI), were used for constructing the molecular phylogenetic trees. Both NJ and BI trees indicated that all Lepturichthys specimens formed as a monophyletic group; the L. dolichopterus samples also formed as monophyletic group, having a derived position in the phylogenetic trees, while the L. fimbriata samples formed as a paraphyletic group. Both L. fimbriata and L. dolichopterus are valid species in morphology. Based on molecular and morphological data, we presumed that the geographical speciation process of the genus Lepturichthys could be as following: during the Quaternary Glacial period, L. fimbriata in the Middle and Lower Yangtze River dispersed to the drainages of Southeast China along the Continental Shelf of East China Sea, one population spread to the Minjiang River and envolved as a new species (L. dolichopterus) because of considerable environmental difference, while the remaining L. fimbriata populations in the Yangtze River formed as a paraphyly. The other similar geographical speciation patterns are discussed in the present study as well.