In order to study the phylogenetic relationship among different species in the order of Siluriformes, ribosomal 18S sequences and internal transcribed spacer (including complete ITS1,5. 8S and ITS2) sequences of six species Siluriformes (Pelteobagrus fulvidraco,Leiocassis longirostris,Mystus guttatus,Clarias gariepinus, Silurus asotus and Ictalurus punctatus) were analyzed. The homologous sequences of Kryptopterus bicirrhis and Dinotopterus cunningtoni download from GenBank were also analyzed in this paper. The length of 18S sequences of these six species was 1 814-1 842 bp. The homology was over 97% . The length of 5. 8S was 157 bp. The homology was 99. 36%-100% . The length of ITS1 was 335-620 bp,with the P. fulvidraco’s the longest,and the I. punctatus’s the shortest; The length of ITS2 was 265-459 bp,with the D. cunningtoni’s the longest,and the I. punctatus’s the shortest. The homology of each ITS1 sequence was 29. 45%-88. 21% ,with the highest between C. gariepinus and D. cunningtoni,and the lowest between S. asotus and C. gariepinus. The homology of each ITS2 sequence was 41. 59%-94. 07% ,with the highest between C. gariepinus and D. cunningtoni,and the lowest between S. asotus and C. gariepinus. Phylogenetic tree based on the 18S and ITS sequences of the eight species,including Cyprinus carpio as an outgroup,was constructed by neighbor-joining method (NJ). The results showed that the relationship between Siluridae and Clariidae was the closest,and Bagridae had a little further relationship with Siluridae and Clariidae among the 4 families in this paper. Ictaluridae had the furthest relationship with the other three families. In Bagridae,Leiocassis was close with Pelteobagrus,while Mystus was a little further with them. In Clariidae,Clarias was very close with Dinotopterus. In Siluridae, Silurus had a far relationship with Kryptopterus.