Abstract: Partial sequences of 16S rRNA genes and mitochondrial cytochrome oxidase subunit I (COI) genes from 12 highly valuable ornamental fish species were amplified using universal primers. The species included the red-tail golden arowana, the yellow-tail arowana, the green arowana, Scleropages formosus, Scleropages jardinii, Osteoglossum bicirrhosum, Pterophyllum scalare, Hemichromis letourneuxi, Aulonocara stuartgranti, Helostoma temminkii, Poecilia reticulate and Trichopodus leerii. The homology and phylogenetic analyses on the genes were carried out by using DNA sequence analysis software, and compared with the databases at GenBank and Bold Systems. The sequence analysis indicated that the information on 16S rRNA and COI genes might be applicable for distinguishing S. formosus, S. jardinii, O. bicirrhosum and P. reticulatefrom one another. However, the phylogenetic tree constructed with the COI gene would be more closely related to the conventional classification than 16S rRNA. Regardless, the use of 16S rRNA and/or COI gene was not deemed sufficient to differentiate or identify very similar genera or species, such as cichlids or different lines of a same species, nor among the red-tail arowana, the yellow-tail arowana and the green arowana. It was suggested that DNA barcoding with higher evolution rate be studied to overcome the shortcoming of the current method.