The Elongate loach (Leptobotia elongata) belongs to family Cobitidae, which is endemic to the middle and upper reaches of the Yangtze River in China. In this study, the complete mitochondrial genome of L. elongata was sequenced. It was determined to be 16,591 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of L. elongata and other 12 Cobitidae species were used for phylogenetic analyses. Trees constructed using Bayesian and maximum parsimony showed a similar topology demonstrating that L. elongate was clustered in subfamily Botiinae being sister to the subfamily Cobitinae. The trees also suggested that the genera Cobitis were polyphyletic.