Abstract: We compare and study the genetic diversity and structure of DNA control region of 4 Misgurnus anguillicaudatus populations by using PCR and DNA sequencing. The results show that the sequence of mitochondrial DNA control region is 918~920 bp.Among 32 sequences, a total of 56 polymorphic loci were detected, including 32 transitions, 19 transversions, 5 transitions-transversions and 36 haplotypes. The key sequences of extended terminal associated sequences (ETAS), central domains (CSB-A, B, C, D, E and F) and conserved sequence blocks (CSB-1, CSB-2 and CSB-3) were discovered. The haplotypic diversity (Hd), average genetic distance (Pi) and average number of pairwise differences (K) is 0.992, 0.012 and 10.698, respectively. The average Kimura 2-parameter distance, F_st value, N_m value and AMOVA reveal great genetic differentiation among the 4 M.anguillicaudatus populations. The NJ phylogenetic tree constructed on nucleotide sequence indicates that the 4 populations form into 2 monophyletic lineages, and cross and cluster among one another except Fanxian population.