This study cloned the complete mitochondrial genome sequences of Megalobrama skolkovii,M.pellegrini and M.terminalis based on the complete mitochondrial genome sequences of M. amblycephala and partial mitochondrial genome sequences of M.hoffmanni,M.ellegrini and M.terminalis in the GenBank database.The complete mitochondrial genome sequences of four species in the genus Megalobrama were analyzed.Results showed that all the mitochondrial genomes of the four Megalobrama fishes contained 13 protein-coding genes,22 tRNA genes,2 rRNA genes,a non-coding control region(D-loop)and a replication origin region of the light chain(OL),with identical arrangement and tightly packed.Eight tRNAs and ND6 genes were encoded on the light strand(L strand),and the remainders encoded on the heavy strand(H strand).All 13 protein-coding genes of the mitochondrial genomes from four species of the genus Megalobrama showed a strong bias toward A+T and a bias for C nucleotides.The comparison of the complete mitochondrial genome sequences showed that there were 758 variable sites,including 691 singleton variable sites(accounting for 91.19%),67 parsimony informative sites(only accounting for 8.84%).Eleven of 22 tRNA genes had mutated in Megalobrama,and 23 variable sites were mainly distributed in the TΨC and DHU of the cloverleaf secondary structure.Additionally,626 variable sites of the protein-coding genes were mainly distributed in the third codon position(accounting for 82.59%)and Cyt b gene had the largest number of different loci(84),followed by ND4 gene with 83 loci.Therefore,Cyt b and ND4 could be used as alternative molecular markers for genetics research in the genus Megalobrama groups,which provided a theoretical and technical basis for the rational and efficient use of biological resources and conservation of biological diversity.Both ML and BI phylogenetic trees based on the complete mitochondrial genome sequences from four species showed that M.terminalis and M.pellegrini had the closest genetic relationship,with M.amblycephala being more closely related to them,and M.hoffmanni was farther related to the other species.