Ribosomal DNA is usually selected as molecular marker for phylogenetic study and the sequence variances especially in IGS region can affect the growth rate of organisms to certain extent. A complete rDNA of Chinese mitten crab (Eriocheir sinensis) was isolated in this study. The rDNA is 11 660 bp in size and consists of 18S(1 873 bp), ITS1(317 bp), 5.8S(163 bp), ITS2(614 bp), 28S(4 461 bp) and IGS(4 240bp). The (AT) contents of different regions range from 40.1% to 48.6%, which are lower than those in Drosophila melanogaster (55.8%-80.0%) and higher than Cyprinus carpio (22.0%-43.7%).The SSR loci per 100 nucleotides in the sequence of descending are ITS-2(0.98%), IGS(0.49%), 28S(0.38%), ITS-1(0.32%), 18S(0.21%), 5.8S(0%).The results of ITS2 intra-variances analysis showed that two types of ITS-2 existed in Chinese mitten crab, with a 12 bp(CGCAGGACCACC) insertion at 405 nt. The IGS region is 4 240 bp in size and there are 136-139 bp speciesspecific repeats that contain an Xho I restriction site. And a stemloop structure (182 pairs stem and 21 nucleotides loop) is located following the specific repeats. The sequence of rDNA in the Chinese mitten crab will provide the foundation of studying the variances among different geographical populations and exploring the molecular marker associated with the fast growth rate of the Chinese mitten crab.