The present study examined the genetic variation in the mitochondrial 12S rRNA, 16S rRNA and cytochromec oxidase subunit 3 (cox3) genes among three varieties of Scleropages formosus, and their phylogenetic relationships were constructed. Among all the examined isolates of S. formosus, sequence variation ranged from 0 to 1.66% for 12S, from 0 to 2.4% for 16S and from 0 to 3.2% for pcox3. AMOVA analysis of the three mtDNA genes showed that the majority of the total molecular variation occurred among varieties within the groups (55.6%) with 48.4% of variation within the varieties. Additionally, a significant genetic differentiation (P < 0.05) was revealed within S. formosus. Phylogenetic analysis based on the combined sequences showed that all S. formosus clustered together and effectively grouped the green arowanas together. These results demonstrate that the three mtDNA sequences are polymorphic but are not suitable markers for comparing the genetic relationships among the different varieties of S. formosus.