The taxonomy of Symphysodon is mainly based on morphology,however,there has been some disagreement on whether one species or two about this genus.In order to study the phylogenetic relationship of Symphysodon and probe into its taxonomy status on molecular level,we sequenced and compared 276 base pairs of mitochondrial D-loop gene sequences from S.aequifasciata aequifasciata,S.a.axelrodi and S.discus,phylogenetic trees were constructed with neighbor-joining method and unweighted pair group method and obtained the same topology.The results showed that: The genetic distance of the 276 bp D-loop gene sequence was 0.004-0.015 among individuals of S.discus;0.042-0.050 between S.a.aequifasciata and S.discus,0.034-0.038 between S.a.axelrodi and S.discus,and 0.050 between S.a.aequifasciata and S.a.axelrodi.The difference between two species of S.discus and S.aequifasciata was close to that of two subspecies between S.a.aequifasciata and S.a.axelrodi,which indicated that S.discus perhaps had not evolved to the level of species.