The complete mitochondrial genome of the typical cave-dwelling nemacheilid loath species, Triplophysa xiangxiensis, was sequenced. The mitogenome of this blind fish, with 16 598 by in length, composed of 13 protein-coding, 2 rRNA and 22 tRNA genes, and 2 non-coding regions (D-loop and O-L). Its phylogenetic position within the Nemacheilidae was estimated. Phylogenetic tree inferred based on the complete mitogenome indicated that T. xiangxiensis was sister to T. rosa; both clustered with all other analyzed congeneric species to form the sister group of sampled species of Barbatula. The pairwise genetic distance between these two blind species was much lower than those between both and all other congeneric species. A further study on the taxonomic status of both within Triplophysa or the Nemacheilidae is warranted.