Amplification and sequence of the β-actin gene of Sinopotamon yangtsekiense were conducted with the reverse transcription polymerase chain reaction (RTPCR). It is aligned with homologous sequences of 6 other crabs from GenBank. The results showed there were 115 variable sites and 57 singleton sites in β-actin homologous sequences of 338 bp. Substitution rates among nucleotide sites were from 1.6％ to 25.3％ and the numbers of nucleotide transitions / transversions were from 0.740 to 4.050. Scylla serrata was more closely related to the sand crab Portunus pelagicus than any other species. S.yangtsekiense was farther related to Gecarcinus lateralis， Neohelice granulate. Furthermore,Eriocheir sinensis was farther related to P.pelagicus. The phylogenetic trees constructed by neighbor joining (NJ) and maximum likelihood (ML) supported the same topology. The phylogenetic analysis implied that S.yangtsekiense was singleton branch, far away from other marine crabs, so it should belong to potamidea. S.serrata was clustered with P.pelagicus firstly, clustered with G.lateralis consequently and then N.granulate was clustered into them. The results of inferred phylogeny were different from traditional classification scheme based on morphology.