The mitochondrial genome can provide useful information for analyzing phylogeny and molecular evolution. In this study, the mitochondrial genome of Aphyocypris lini, an endangered and endemic minnow from southeast China, was sequenced and compared with other closely related species. The mitogenome of A. lini is 16,613 base pairs in length and consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one displacement loop region. All of PCGs initiate with the standard start codon ATG except cox1 with GTG and most PCGs terminate with TAA or TAG. The genome composition is highly A + T biased (57.3%), and exhibits a positive AT-skew (0.0614) and a negative GC-skew (−0.2205). Based on PCGs, phylogenetic analysis showed that former Ex-Danioninae subfamily was reclassified as Xenocyprididae and divided into two main clades: Opsariichthyinae and Xenocypridinae. Within Xenocypridinae, genus Aphyocypris is not monophyletic but closely related to Yaoshanicus, Nicholsicypris, and Pararasbora genera, suggesting taxonomy should be reconsidered. The present study contributes to understanding the comparative evolution and taxonomy of genus Aphyocypris.