Mitochondrial DNA control region of Schizothorax prenanti was sequenced and analyzed by comparing with other species. The content of A and T in the control region of S.prenanti was higher than that of G and C. Compared with mammals and other species of Cypriniformes, several conserved sequence blocks were identified in the mitochondrial DNA control region of S.prenanti, including extended terminal associated sequences (ETAS), blocks of central domain (F, E, D, B-box) and conserved sequence block (CSB1-3).