Abstract: Xenocypridinae, as one of the benthic fishes of Cyprinidae (Cypriniformes) in East Asia, contains three genera of about nine species and is one of the smallest subfamilies in Cyprinidae. Despite the small number of species, the phylogenetic relationships of Xenocypridinae still lack a valid and extensive assessment. To this end, this study assessed the phylogenetic relationships and divergence times between members of the subfamily Xenocypridinae using a variety of phylogenetic approaches based on two mitochondrial genes and five nuclear genes. The results showed that analyses based on maximum likelihood and Bayesian approaches harvest consistent topologies, but there are some conflicts in the results based on different datasets. In particular, the monophyly of each of the three genera was well supported in all analyses, but the evolutionary relationships between them were discordant between the results based on mitochondrial and nuclear genes. Analyses based on the coalescent algorithm yielded a third phylogenetic relationship among the genera. These results implied that both ancient gene flow and lineage sorting influenced the relationships between deep clades of the subfamily Xenocypridinae. Additionally, these analyses give insights into the classification of these species, for example, Xenocypris hupeinensis should belong to the genus Xenocypris; the nested relationships among species X. argentea, X. yunnanensis, and X. davidi suggest the possibility of gene flow and the need for taxonomic reconsideration. Finally, a fossil-based molecular clock assessment indicates that the divergence of key Xenocypridinae clades occurred mainly in the late Miocene (ca. 15—12 Ma), which coincides with the intensification of the Asian monsoon and supports the hypothesis that the ichthyofauna of East Asia was established in the early Pliocene and flourished to date. In summary, this study has systematically assessed the phylogeny of Xenocypridinae and made recommendations for future work.