Mitochondrial control region was called "A + T-rich" region in invertebrate. In the study, the general organization of control region in mitten crab was divided into two major domains: high variable segment and conserved segment. Four conserved blocks (CSB1, CSB2, CSB3 and CSB4) and two tandem repeat sequences (RT1 and RT2) were defined in control region. There were 116 polymorphic sites and 84 parsimony information sites in 571 aligned sites of the high variable segment adjacent "tRNA-Gln", in which 58 stable variable sites were defined between E. j. sinensis and E. j. hepuensis. Conserved domain contained more than two similar repeat units, and length polymorphism of control region was due to the number difference between the two repeat units (RT1 and RT2). And length polymorphism was a common phenomenon for tandem repeat in control region in the study. Furthermore, a novel result showed the core nucleotide of RT2 in control region tandem repeat was C in E. j. hepuensis, but G in E. j. sinensis. It might be a rapid and cost-effective measure of seedlings differentiation in aquaculture.