Myodes rufocanus and M.rutilus have overlapping range and similar morphological characteristics.It is hard to distinguish these two species under some conditions,which brings inconvenience and miscalculation to their number investigations.Eight known samples and sixteen unknown samples of M.rufocanus and M.rutilus are correctly identified by three molecular methods:phylogenetic tree based on sequences of mtDNA control region,electrophoresis of mtDNA control region,and the RAPD).Electrophoresis of mtDNA control region shows the advantages of convenience,accuracy and time-saving.