Corals are the dominant species of the coral reefs. The diversity of species is classified by traditional morphological traits, especially relied on the calcious deposits-sclerites. The formation of sclerites may be affected by the environmental conditions; therefore, some controversies may exist. The ambiguities may be clarified with molecular approaches. Five soft coral species, Lobophytum pauciflorum, Sinularia leptoclado, Sinularia flexibilis, Sarcophyton sp., Nephthea erecta were chosen for this study. The total mitochondrial DNA sequences were determined by PCR and primer walking. The genome contains 18562 bp, 18732 bp, 18752 bp, 18806 bp, 18716 bp separately, which harbors 14 protein-coding genes (ATP6¡BATP8¡BCOI¡BCOII¡BCOIIII¡BCYTB¡BND1¡BND2¡BND3¡BND4¡BND4L¡BND5¡BND6¡BMSH), 2 rRNA and only 1 tRNA genes. The phylogenetic relationship of alcyonacea corals were analyzed and compared with published sequences. The possibility of using a short ¡§DNA bar-code sequence¡¨ of the mitochondria as an alternative for species identification may be feasible. We found the short DNA signature sequences for these five corals. They may speed up the identification of corals in the long run.